From 85c968d766eed5d9bb7ec4e7d9fad00b288156b8 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 25 Sep 2024 17:34:43 +0200 Subject: [PATCH 01/36] update dependency versions --- tools/idr_download/idr_download_by_ids.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml index 26af1ddf947..5e3395043dc 100644 --- a/tools/idr_download/idr_download_by_ids.xml +++ b/tools/idr_download/idr_download_by_ids.xml @@ -1,5 +1,5 @@ - + @@ -19,8 +19,8 @@ operation_3443 - omero-py - pylibtiff + omero-py + pylibtiff Date: Wed, 25 Sep 2024 17:36:17 +0200 Subject: [PATCH 02/36] enable download of the full image (hyperstack) --- tools/idr_download/idr_download_by_ids.py | 148 ++++++++++++++------- tools/idr_download/idr_download_by_ids.xml | 101 ++++++++++---- 2 files changed, 177 insertions(+), 72 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 6c2adddf345..a399cc699af 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -5,7 +5,10 @@ import tarfile from contextlib import ExitStack from tempfile import TemporaryDirectory +from itertools import product +import numpy +from tifffile import imwrite from libtiff import TIFF from omero.cli import cli_login from omero.gateway import BlitzGateway # noqa @@ -110,9 +113,27 @@ def get_image_array(image, tile, z, c, t): return selection +def get_full_image_array(image): + # The goal is to get the image in TZCYX order + pixels = image.getPrimaryPixels() + tzclist = list(product(range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC()))) + zctlist = [(z, c, t) for (t, z, c) in tzclist] + try: + all_planes = numpy.array(list(pixels.getPlanes(zctlist))) + all_planes_reshaped = all_planes.reshape(image.getSizeT(), image.getSizeZ(), image.getSizeC(), all_planes.shape[-2], all_planes.shape[-1]) + except Exception as e: + warning = '{0} (ID: {1})'.format(image.getName(), + image.getId()) + warn('Could not download the requested region', warning) + warn(e.msg) + return + + return all_planes_reshaped + + def download_image_data( image_ids_or_dataset_id, dataset=False, - download_original=False, + download_original=False, download_full=False, channel=None, z_stack=0, frame=0, coord=(0, 0), width=0, height=0, region_spec='rectangle', skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None @@ -131,7 +152,7 @@ def download_image_data( omero_username = 'public' omero_password = 'public' - if not download_original and region_spec not in ['rectangle', 'center']: + if not download_original and not download_full and region_spec not in ['rectangle', 'center']: raise ValueError( 'Got unknown value "{0}" as region_spec argument' .format(region_spec) @@ -226,16 +247,79 @@ def download_image_data( 'database. Aborting!' .format(image_warning_id) ) - if not download_original: + try: + # try to extract image name + # if anything goes wrong here skip the image + # or abort. + image_name = os.path.splitext(image.getName())[0] + image_warning_id = '{0} (ID: {1})'.format( + image_name, image_id + ) + except Exception as e: + # respect skip_failed on unexpected errors + if skip_failed: + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise + if download_full: + fname = '__'.join([image_name.replace(' ', '_'), str(image_id), "full"]) + '.tiff' + # download and save the region as TIFF + try: + im_array = get_full_image_array(image) + + if download_tar: + fname = os.path.join(tempdir, fname) + + imwrite(fname, im_array, imagej=True) + # move image into tarball + if download_tar: + archive.add(fname, os.path.basename(fname)) + os.remove(fname) + except Exception as e: + if skip_failed: + # respect skip_failed on unexpected errors + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise + + elif download_original: + try: + # try to extract image properties + # if anything goes wrong here skip the image + # or abort. + original_image_name = image.getFileset().listFiles()[0].getName() + fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1] + fname = fname.replace(' ', '_') + fname = fname.replace('/', '_') + download_directory = "./" + if download_tar: + download_directory = tempdir + with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli: + cli.invoke(["download", f"Image:{image_id}", download_directory]) + if cli.rv != 0: + raise Exception("Download failed.") + # This will download to download_directory/original_image_name + os.rename(os.path.join(download_directory, original_image_name), + os.path.join(download_directory, fname)) + # move image into tarball + if download_tar: + archive.add(os.path.join(download_directory, fname), + os.path.basename(fname)) + os.remove(os.path.join(download_directory, fname)) + except Exception as e: + # respect skip_failed on unexpected errors + if skip_failed: + warn(str(e), image_warning_id, warn_skip=True) + continue + else: + raise + else: try: # try to extract image properties # if anything goes wrong here skip the image # or abort. - image_name = os.path.splitext(image.getName())[0] - image_warning_id = '{0} (ID: {1})'.format( - image_name, image_id - ) - if region_spec == 'rectangle': tile = get_clipping_region(image, *coord, width, height) elif region_spec == 'center': @@ -314,16 +398,13 @@ def download_image_data( .format(channel, image_warning_id) ) - # download and save the region as TIFF fname = '__'.join( [image_name, str(image_id)] + [str(x) for x in tile] ) + fname += '.tiff' + fname = fname.replace(' ', '_') + # download and save the region as TIFF try: - if fname[-5:] != '.tiff': - fname += '.tiff' - - fname = fname.replace(' ', '_') - im_array = get_image_array(image, tile, z_stack, channel_index, frame) if download_tar: @@ -344,41 +425,6 @@ def download_image_data( continue else: raise - else: - try: - # try to extract image properties - # if anything goes wrong here skip the image - # or abort. - image_name = os.path.splitext(image.getName())[0] - image_warning_id = '{0} (ID: {1})'.format( - image_name, image_id - ) - original_image_name = image.getFileset().listFiles()[0].getName() - fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1] - fname = fname.replace(' ', '_') - fname = fname.replace('/', '_') - download_directory = "./" - if download_tar: - download_directory = tempdir - with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli: - cli.invoke(["download", f"Image:{image_id}", download_directory]) - if cli.rv != 0: - raise Exception("Download failed.") - # This will download to download_directory/original_image_name - os.rename(os.path.join(download_directory, original_image_name), - os.path.join(download_directory, fname)) - # move image into tarball - if download_tar: - archive.add(os.path.join(download_directory, fname), - os.path.basename(fname)) - os.remove(os.path.join(download_directory, fname)) - except Exception as e: - # respect skip_failed on unexpected errors - if skip_failed: - warn(str(e), image_warning_id, warn_skip=True) - continue - else: - raise def _center_to_ul(center_x, center_y, width, height): @@ -409,6 +455,10 @@ def _center_to_ul(center_x, center_y, width, height): '--download-original', dest='download_original', action='store_true', help="download the original file uploaded to omero" ) + p.add_argument( + '--download-full', dest='download_full', action='store_true', + help="download the full image on omero" + ) p.add_argument( '-c', '--channel', help='name of the channel to retrieve data for ' diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml index 5e3395043dc..f42af81814b 100644 --- a/tools/idr_download/idr_download_by_ids.xml +++ b/tools/idr_download/idr_download_by_ids.xml @@ -21,6 +21,7 @@ omero-py pylibtiff + tifffile - + + + - + @@ -202,10 +207,10 @@ - + - + @@ -225,10 +230,10 @@ - + - + @@ -248,10 +253,10 @@ - + - + @@ -270,7 +275,11 @@ - + + + + + @@ -299,7 +308,7 @@ - + @@ -321,7 +330,11 @@ - + + + + + @@ -333,7 +346,7 @@ - + @@ -354,17 +367,25 @@ - + - + + + + + - + + + + + - + @@ -387,7 +408,7 @@ - + @@ -415,7 +436,7 @@ - + @@ -426,27 +447,43 @@ - + + + + + - + + + + + - + + + + + - + + + + + - + @@ -462,6 +499,24 @@ + + + + + + + + + + + + + + + + + + Date: Wed, 25 Sep 2024 17:36:47 +0200 Subject: [PATCH 03/36] run isort --- tools/idr_download/idr_download_by_ids.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index a399cc699af..f630b1feb29 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -4,15 +4,15 @@ import sys import tarfile from contextlib import ExitStack -from tempfile import TemporaryDirectory from itertools import product -import numpy +from tempfile import TemporaryDirectory -from tifffile import imwrite +import numpy from libtiff import TIFF from omero.cli import cli_login -from omero.gateway import BlitzGateway # noqa from omero.constants.namespaces import NSBULKANNOTATIONS # noqa +from omero.gateway import BlitzGateway # noqa +from tifffile import imwrite def warn(message, image_identifier, warn_skip=False): From 62767452d5453019198cdf1d466765fbe3411d20 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 25 Sep 2024 17:36:59 +0200 Subject: [PATCH 04/36] run black --- tools/idr_download/idr_download_by_ids.py | 344 ++++++++++++---------- 1 file changed, 181 insertions(+), 163 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index f630b1feb29..62e599f9373 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -18,20 +18,15 @@ def warn(message, image_identifier, warn_skip=False): message = message.rstrip() if warn_skip: - if message[-1] in ['.', '!', '?']: - skip_msg = ' Skipping download!' + if message[-1] in [".", "!", "?"]: + skip_msg = " Skipping download!" else: - skip_msg = '. Skipping download!' + skip_msg = ". Skipping download!" else: - skip_msg = '' + skip_msg = "" print( - 'ImageSpecWarning for {0}: {1}{2}' - .format( - image_identifier, - message, - skip_msg - ), - file=sys.stderr + "ImageSpecWarning for {0}: {1}{2}".format(image_identifier, message, skip_msg), + file=sys.stderr, ) @@ -47,7 +42,7 @@ def find_channel_index(image, channel_name): if p[0] == "Channels": channels = p[1].replace(" ", "").split(";") for n, c in enumerate(channels): - for value in c.split(':'): + for value in c.split(":"): if channel_name == value.lower(): return n return -1 @@ -61,16 +56,16 @@ def get_clipping_region(image, x, y, w, h): # It may be better to abort in this situation. if x < 0 or y < 0: raise ValueError( - 'Too small upper left coordinate ({0}, {1}) for clipping region.' - .format(x, y) + "Too small upper left coordinate ({0}, {1}) for clipping region.".format( + x, y + ) ) size_x = image.getSizeX() size_y = image.getSizeY() if x >= size_x or y >= size_y: raise ValueError( - 'Upper left coordinate ({0}, {1}) of clipping region lies ' - 'outside of image.' - .format(x, y) + "Upper left coordinate ({0}, {1}) of clipping region lies " + "outside of image.".format(x, y) ) # adjust width and height to the image dimensions if w <= 0 or x + w > size_x: @@ -105,9 +100,8 @@ def get_image_array(image, tile, z, c, t): try: selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile) except Exception: - warning = '{0} (ID: {1})'.format(image.getName(), - image.getId()) - warn('Could not download the requested region', warning) + warning = "{0} (ID: {1})".format(image.getName(), image.getId()) + warn("Could not download the requested region", warning) return return selection @@ -116,15 +110,24 @@ def get_image_array(image, tile, z, c, t): def get_full_image_array(image): # The goal is to get the image in TZCYX order pixels = image.getPrimaryPixels() - tzclist = list(product(range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC()))) + tzclist = list( + product( + range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC()) + ) + ) zctlist = [(z, c, t) for (t, z, c) in tzclist] try: all_planes = numpy.array(list(pixels.getPlanes(zctlist))) - all_planes_reshaped = all_planes.reshape(image.getSizeT(), image.getSizeZ(), image.getSizeC(), all_planes.shape[-2], all_planes.shape[-1]) + all_planes_reshaped = all_planes.reshape( + image.getSizeT(), + image.getSizeZ(), + image.getSizeC(), + all_planes.shape[-2], + all_planes.shape[-1], + ) except Exception as e: - warning = '{0} (ID: {1})'.format(image.getName(), - image.getId()) - warn('Could not download the requested region', warning) + warning = "{0} (ID: {1})".format(image.getName(), image.getId()) + warn("Could not download the requested region", warning) warn(e.msg) return @@ -132,51 +135,59 @@ def get_full_image_array(image): def download_image_data( - image_ids_or_dataset_id, dataset=False, - download_original=False, download_full=False, - channel=None, z_stack=0, frame=0, - coord=(0, 0), width=0, height=0, region_spec='rectangle', - skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=False, config_file=None + image_ids_or_dataset_id, + dataset=False, + download_original=False, + download_full=False, + channel=None, + z_stack=0, + frame=0, + coord=(0, 0), + width=0, + height=0, + region_spec="rectangle", + skip_failed=False, + download_tar=False, + omero_host="idr.openmicroscopy.org", + omero_secured=False, + config_file=None, ): if config_file is None: # IDR connection - omero_username = 'public' - omero_password = 'public' + omero_username = "public" + omero_password = "public" else: # other omero instance with open(config_file) as f: cfg = json.load(f) - omero_username = cfg['username'] - omero_password = cfg['password'] + omero_username = cfg["username"] + omero_password = cfg["password"] if omero_username == "" or omero_password == "": - omero_username = 'public' - omero_password = 'public' - - if not download_original and not download_full and region_spec not in ['rectangle', 'center']: + omero_username = "public" + omero_password = "public" + + if ( + not download_original + and not download_full + and region_spec not in ["rectangle", "center"] + ): raise ValueError( - 'Got unknown value "{0}" as region_spec argument' - .format(region_spec) + 'Got unknown value "{0}" as region_spec argument'.format(region_spec) ) with ExitStack() as exit_stack: conn = exit_stack.enter_context( BlitzGateway( - omero_username, omero_password, - host=omero_host, - secure=omero_secured + omero_username, omero_password, host=omero_host, secure=omero_secured ) ) # exit_stack.callback(conn.connect().close) if download_tar: # create an archive file to write images to - archive = exit_stack.enter_context( - tarfile.open('images.tar', mode='w') - ) - tempdir = exit_stack.enter_context( - TemporaryDirectory() - ) + archive = exit_stack.enter_context(tarfile.open("images.tar", mode="w")) + tempdir = exit_stack.enter_context(TemporaryDirectory()) if dataset: - dataset_warning_id = 'Dataset-ID: {0}'.format(image_ids_or_dataset_id[0]) + dataset_warning_id = "Dataset-ID: {0}".format(image_ids_or_dataset_id[0]) try: dataset_id = int(image_ids_or_dataset_id[0]) except ValueError: @@ -196,28 +207,26 @@ def download_image_data( if image_ids is None: if skip_failed: warn( - 'Unable to find a dataset with this ID in the ' - 'database.', + "Unable to find a dataset with this ID in the " "database.", dataset_warning_id, - warn_skip=True + warn_skip=True, ) else: raise ValueError( - '{0}: Unable to find a dataset with this ID in the ' - 'database. Aborting!' - .format(dataset_warning_id) + "{0}: Unable to find a dataset with this ID in the " + "database. Aborting!".format(dataset_warning_id) ) else: # basic argument sanity checks and adjustments - prefix = 'image-' + prefix = "image-" # normalize image ids by stripping off prefix if it exists image_ids = [ - iid[len(prefix):] if iid[:len(prefix)] == prefix else iid + iid[len(prefix) :] if iid[: len(prefix)] == prefix else iid for iid in image_ids_or_dataset_id ] for image_id in image_ids: - image_warning_id = 'Image-ID: {0}'.format(image_id) + image_warning_id = "Image-ID: {0}".format(image_id) try: image_id = int(image_id) except ValueError: @@ -236,25 +245,21 @@ def download_image_data( if image is None: if skip_failed: warn( - 'Unable to find an image with this ID in the ' - 'database.', + "Unable to find an image with this ID in the " "database.", image_warning_id, - warn_skip=True + warn_skip=True, ) continue raise ValueError( - '{0}: Unable to find an image with this ID in the ' - 'database. Aborting!' - .format(image_warning_id) + "{0}: Unable to find an image with this ID in the " + "database. Aborting!".format(image_warning_id) ) try: # try to extract image name # if anything goes wrong here skip the image # or abort. image_name = os.path.splitext(image.getName())[0] - image_warning_id = '{0} (ID: {1})'.format( - image_name, image_id - ) + image_warning_id = "{0} (ID: {1})".format(image_name, image_id) except Exception as e: # respect skip_failed on unexpected errors if skip_failed: @@ -263,7 +268,10 @@ def download_image_data( else: raise if download_full: - fname = '__'.join([image_name.replace(' ', '_'), str(image_id), "full"]) + '.tiff' + fname = ( + "__".join([image_name.replace(" ", "_"), str(image_id), "full"]) + + ".tiff" + ) # download and save the region as TIFF try: im_array = get_full_image_array(image) @@ -290,23 +298,36 @@ def download_image_data( # if anything goes wrong here skip the image # or abort. original_image_name = image.getFileset().listFiles()[0].getName() - fname = image_name + "__" + str(image_id) + os.path.splitext(original_image_name)[1] - fname = fname.replace(' ', '_') - fname = fname.replace('/', '_') + fname = ( + image_name + + "__" + + str(image_id) + + os.path.splitext(original_image_name)[1] + ) + fname = fname.replace(" ", "_") + fname = fname.replace("/", "_") download_directory = "./" if download_tar: download_directory = tempdir - with cli_login("-u", omero_username, "-s", omero_host, "-w", omero_password) as cli: - cli.invoke(["download", f"Image:{image_id}", download_directory]) + with cli_login( + "-u", omero_username, "-s", omero_host, "-w", omero_password + ) as cli: + cli.invoke( + ["download", f"Image:{image_id}", download_directory] + ) if cli.rv != 0: raise Exception("Download failed.") # This will download to download_directory/original_image_name - os.rename(os.path.join(download_directory, original_image_name), - os.path.join(download_directory, fname)) + os.rename( + os.path.join(download_directory, original_image_name), + os.path.join(download_directory, fname), + ) # move image into tarball if download_tar: - archive.add(os.path.join(download_directory, fname), - os.path.basename(fname)) + archive.add( + os.path.join(download_directory, fname), + os.path.basename(fname), + ) os.remove(os.path.join(download_directory, fname)) except Exception as e: # respect skip_failed on unexpected errors @@ -320,12 +341,11 @@ def download_image_data( # try to extract image properties # if anything goes wrong here skip the image # or abort. - if region_spec == 'rectangle': + if region_spec == "rectangle": tile = get_clipping_region(image, *coord, width, height) - elif region_spec == 'center': + elif region_spec == "center": tile = get_clipping_region( - image, - *_center_to_ul(*coord, width, height) + image, *_center_to_ul(*coord, width, height) ) ori_z, z_stack = z_stack, confine_plane(image, z_stack) @@ -348,69 +368,66 @@ def download_image_data( # The downloaded image region will have smaller dimensions # than the specified width x height. warn( - 'Downloaded image dimensions ({0} x {1}) will be smaller ' - 'than the specified width and height ({2} x {3}).' - .format(tile[2], tile[3], width, height), - image_warning_id + "Downloaded image dimensions ({0} x {1}) will be smaller " + "than the specified width and height ({2} x {3}).".format( + tile[2], tile[3], width, height + ), + image_warning_id, ) # z-stack sanity checks and warnings if z_stack != ori_z: warn( - 'Specified image plane ({0}) is out of bounds. Using {1} ' - 'instead.' - .format(ori_z, z_stack), - image_warning_id + "Specified image plane ({0}) is out of bounds. Using {1} " + "instead.".format(ori_z, z_stack), + image_warning_id, ) # frame sanity checks and warnings if frame != ori_frame: warn( - 'Specified image frame ({0}) is out of bounds. Using ' - 'frame {1} instead.' - .format(ori_frame, frame), - image_warning_id + "Specified image frame ({0}) is out of bounds. Using " + "frame {1} instead.".format(ori_frame, frame), + image_warning_id, ) # channel index sanity checks and warnings if channel is None: if num_channels > 1: warn( - 'No specific channel selected for multi-channel ' - 'image. Using first of {0} channels.' - .format(num_channels), - image_warning_id + "No specific channel selected for multi-channel " + "image. Using first of {0} channels.".format(num_channels), + image_warning_id, ) else: if channel_index == -1 or channel_index >= num_channels: if skip_failed: warn( str(channel) - + ' is not a known channel name for this image.', + + " is not a known channel name for this image.", image_warning_id, - warn_skip=True + warn_skip=True, ) continue else: raise ValueError( '"{0}" is not a known channel name for image {1}. ' - 'Aborting!' - .format(channel, image_warning_id) + "Aborting!".format(channel, image_warning_id) ) - fname = '__'.join( - [image_name, str(image_id)] + [str(x) for x in tile] - ) - fname += '.tiff' - fname = fname.replace(' ', '_') + fname = "__".join([image_name, str(image_id)] + [str(x) for x in tile]) + fname += ".tiff" + fname = fname.replace(" ", "_") # download and save the region as TIFF try: - im_array = get_image_array(image, tile, z_stack, channel_index, frame) + im_array = get_image_array( + image, tile, z_stack, channel_index, frame + ) if download_tar: fname = os.path.join(tempdir, fname) try: - tiff = TIFF.open(fname, mode='w') + tiff = TIFF.open(fname, mode="w") tiff.write_image(im_array) finally: tiff.close() @@ -446,81 +463,82 @@ def _center_to_ul(center_x, center_y, width, height): if __name__ == "__main__": p = argparse.ArgumentParser() p.add_argument( - 'image_ids_or_dataset_id', nargs='*', default=[], - help='one or more IDR image ids or a single dataset id' - 'for which to retrieve data (default: ' - 'read ids from stdin).' + "image_ids_or_dataset_id", + nargs="*", + default=[], + help="one or more IDR image ids or a single dataset id" + "for which to retrieve data (default: " + "read ids from stdin).", ) p.add_argument( - '--download-original', dest='download_original', action='store_true', - help="download the original file uploaded to omero" + "--download-original", + dest="download_original", + action="store_true", + help="download the original file uploaded to omero", ) p.add_argument( - '--download-full', dest='download_full', action='store_true', - help="download the full image on omero" + "--download-full", + dest="download_full", + action="store_true", + help="download the full image on omero", ) p.add_argument( - '-c', '--channel', - help='name of the channel to retrieve data for ' - '(note: the first channel of each image will be downloaded if ' - 'left unspecified)' + "-c", + "--channel", + help="name of the channel to retrieve data for " + "(note: the first channel of each image will be downloaded if " + "left unspecified)", ) region = p.add_mutually_exclusive_group() region.add_argument( - '--rectangle', nargs=4, type=int, default=argparse.SUPPRESS, - help='specify a clipping region for the image as x y width height, ' - 'where x and y give the upper left coordinate of the rectangle ' - 'to clip to. Set width and height to 0 to extend the rectangle ' - 'to the actual size of the image.' + "--rectangle", + nargs=4, + type=int, + default=argparse.SUPPRESS, + help="specify a clipping region for the image as x y width height, " + "where x and y give the upper left coordinate of the rectangle " + "to clip to. Set width and height to 0 to extend the rectangle " + "to the actual size of the image.", ) region.add_argument( - '--center', nargs=4, type=int, default=argparse.SUPPRESS, - help='specify a clipping region for the image as x y width height, ' - 'where x and y define the center of a width x height rectangle. ' - 'Set either width or height to 0 to extend the region to the ' - 'actual size of the image along the x- or y-axis.\n' - 'Note: Even values for width and height will be rounded down to ' - 'the nearest odd number.' - ) - p.add_argument( - '-f', '--frame', type=int, default=0 - ) - p.add_argument( - '-z', '--z-stack', type=int, default=0 - ) - p.add_argument( - '--skip-failed', action='store_true' - ) - p.add_argument( - '--download-tar', action='store_true' - ) - p.add_argument( - '-oh', '--omero-host', type=str, default="idr.openmicroscopy.org" - ) - p.add_argument( - '--omero-secured', action='store_true', default=True - ) - p.add_argument( - '-cf', '--config-file', dest='config_file', default=None - ) - p.add_argument( - '--dataset', action='store_true' + "--center", + nargs=4, + type=int, + default=argparse.SUPPRESS, + help="specify a clipping region for the image as x y width height, " + "where x and y define the center of a width x height rectangle. " + "Set either width or height to 0 to extend the region to the " + "actual size of the image along the x- or y-axis.\n" + "Note: Even values for width and height will be rounded down to " + "the nearest odd number.", ) + p.add_argument("-f", "--frame", type=int, default=0) + p.add_argument("-z", "--z-stack", type=int, default=0) + p.add_argument("--skip-failed", action="store_true") + p.add_argument("--download-tar", action="store_true") + p.add_argument("-oh", "--omero-host", type=str, default="idr.openmicroscopy.org") + p.add_argument("--omero-secured", action="store_true", default=True) + p.add_argument("-cf", "--config-file", dest="config_file", default=None) + p.add_argument("--dataset", action="store_true") args = p.parse_args() if not args.image_ids_or_dataset_id: args.image_ids_or_dataset_id = sys.stdin.read().split() if args.dataset and len(args.image_ids_or_dataset_id) > 1: warn("Multiple dataset ids provided. Only the first one will be used.") - if 'center' in args: + if "center" in args: args.coord, args.width, args.height = ( - args.center[:2], args.center[2], args.center[3] + args.center[:2], + args.center[2], + args.center[3], ) - args.region_spec = 'center' + args.region_spec = "center" del args.center - elif 'rectangle' in args: + elif "rectangle" in args: args.coord, args.width, args.height = ( - args.rectangle[:2], args.rectangle[2], args.rectangle[3] + args.rectangle[:2], + args.rectangle[2], + args.rectangle[3], ) - args.region_spec = 'rectangle' + args.region_spec = "rectangle" del args.rectangle download_image_data(**vars(args)) From b7862310784a2088945d84a3df9942355e4beebc Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 25 Sep 2024 17:37:29 +0200 Subject: [PATCH 05/36] check flake8 --- tools/idr_download/idr_download_by_ids.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 62e599f9373..787e9faaab3 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -222,7 +222,7 @@ def download_image_data( prefix = "image-" # normalize image ids by stripping off prefix if it exists image_ids = [ - iid[len(prefix) :] if iid[: len(prefix)] == prefix else iid + iid[len(prefix):] if iid[:len(prefix)] == prefix else iid for iid in image_ids_or_dataset_id ] for image_id in image_ids: From fe2d7396b32572f248d42606bb0caf44088befe3 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 09:44:40 +0200 Subject: [PATCH 06/36] Apply suggestions from @kostrykin Co-authored-by: Leonid Kostrykin --- tools/idr_download/idr_download_by_ids.py | 4 +--- tools/idr_download/idr_download_by_ids.xml | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 787e9faaab3..d1a60fed189 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -180,7 +180,6 @@ def download_image_data( omero_username, omero_password, host=omero_host, secure=omero_secured ) ) - # exit_stack.callback(conn.connect().close) if download_tar: # create an archive file to write images to archive = exit_stack.enter_context(tarfile.open("images.tar", mode="w")) @@ -245,7 +244,7 @@ def download_image_data( if image is None: if skip_failed: warn( - "Unable to find an image with this ID in the " "database.", + "Unable to find an image with this ID in the database.", image_warning_id, warn_skip=True, ) @@ -291,7 +290,6 @@ def download_image_data( continue else: raise - elif download_original: try: # try to extract image properties diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml index f42af81814b..a56d4f9684d 100644 --- a/tools/idr_download/idr_download_by_ids.xml +++ b/tools/idr_download/idr_download_by_ids.xml @@ -138,7 +138,7 @@ - + From b6f985894293b503ea4a2139f886ba79b20787c1 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 09:46:23 +0200 Subject: [PATCH 07/36] remove noqa --- tools/idr_download/idr_download_by_ids.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index d1a60fed189..d4d0004b16a 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -10,8 +10,8 @@ import numpy from libtiff import TIFF from omero.cli import cli_login -from omero.constants.namespaces import NSBULKANNOTATIONS # noqa -from omero.gateway import BlitzGateway # noqa +from omero.constants.namespaces import NSBULKANNOTATIONS +from omero.gateway import BlitzGateway from tifffile import imwrite From cdebf2a93f4d6441d4aecc5227da1eb44979f670 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 26 Sep 2024 10:15:26 +0200 Subject: [PATCH 08/36] poretools remore --- tools/poretools/poretools_events.xml | 1 - tools/poretools/poretools_extract.xml | 1 - tools/poretools/poretools_hist.xml | 1 - tools/poretools/poretools_nucdist.xml | 1 - tools/poretools/poretools_occupancy.xml | 1 - tools/poretools/poretools_qualdist.xml | 1 - tools/poretools/poretools_squiggle.xml | 1 - tools/poretools/poretools_stats.xml | 1 - tools/poretools/poretools_tabular.xml | 1 - tools/poretools/poretools_times.xml | 1 - tools/poretools/poretools_winner.xml | 1 - tools/poretools/poretools_yield_plot.xml | 1 - 12 files changed, 12 deletions(-) diff --git a/tools/poretools/poretools_events.xml b/tools/poretools/poretools_events.xml index 2d74cf3e343..50ad5aab59c 100644 --- a/tools/poretools/poretools_events.xml +++ b/tools/poretools/poretools_events.xml @@ -1,4 +1,3 @@ - from a set of sequencing reads diff --git a/tools/poretools/poretools_extract.xml b/tools/poretools/poretools_extract.xml index 72fc97f6f7e..d3eefa4425d 100644 --- a/tools/poretools/poretools_extract.xml +++ b/tools/poretools/poretools_extract.xml @@ -1,4 +1,3 @@ - in FASTA or FASTQ format from nanopore files diff --git a/tools/poretools/poretools_hist.xml b/tools/poretools/poretools_hist.xml index 93ff3c9b7d5..49c37aafa72 100644 --- a/tools/poretools/poretools_hist.xml +++ b/tools/poretools/poretools_hist.xml @@ -1,4 +1,3 @@ - of nanopore read lengths diff --git a/tools/poretools/poretools_nucdist.xml b/tools/poretools/poretools_nucdist.xml index 391afe1abe5..662e5450733 100644 --- a/tools/poretools/poretools_nucdist.xml +++ b/tools/poretools/poretools_nucdist.xml @@ -1,4 +1,3 @@ - distribution in nanopore sequencing reads diff --git a/tools/poretools/poretools_occupancy.xml b/tools/poretools/poretools_occupancy.xml index 66fdd505b03..70300d62e2f 100644 --- a/tools/poretools/poretools_occupancy.xml +++ b/tools/poretools/poretools_occupancy.xml @@ -1,4 +1,3 @@ - per cell in nanopore reads diff --git a/tools/poretools/poretools_qualdist.xml b/tools/poretools/poretools_qualdist.xml index 5a9ae6f7f6c..eac45475aab 100644 --- a/tools/poretools/poretools_qualdist.xml +++ b/tools/poretools/poretools_qualdist.xml @@ -1,4 +1,3 @@ - score distribution in nanopore sequencing reads diff --git a/tools/poretools/poretools_squiggle.xml b/tools/poretools/poretools_squiggle.xml index 466b90be6fe..dd16e052860 100644 --- a/tools/poretools/poretools_squiggle.xml +++ b/tools/poretools/poretools_squiggle.xml @@ -1,4 +1,3 @@ - for nanopore reads diff --git a/tools/poretools/poretools_stats.xml b/tools/poretools/poretools_stats.xml index 551ae7acab8..c0e2606ac80 100644 --- a/tools/poretools/poretools_stats.xml +++ b/tools/poretools/poretools_stats.xml @@ -1,4 +1,3 @@ - from a set of FAST5 files diff --git a/tools/poretools/poretools_tabular.xml b/tools/poretools/poretools_tabular.xml index d7668b2fac6..03aea0d1b8b 100644 --- a/tools/poretools/poretools_tabular.xml +++ b/tools/poretools/poretools_tabular.xml @@ -1,4 +1,3 @@ - in tabular format from a set of FAST5 files diff --git a/tools/poretools/poretools_times.xml b/tools/poretools/poretools_times.xml index f4dde2424d4..6ca041cbb0b 100644 --- a/tools/poretools/poretools_times.xml +++ b/tools/poretools/poretools_times.xml @@ -1,4 +1,3 @@ - and channel information from a set of FAST5 files diff --git a/tools/poretools/poretools_winner.xml b/tools/poretools/poretools_winner.xml index 3b84342b238..db027c1881f 100644 --- a/tools/poretools/poretools_winner.xml +++ b/tools/poretools/poretools_winner.xml @@ -1,4 +1,3 @@ - from a set of FAST5 files. diff --git a/tools/poretools/poretools_yield_plot.xml b/tools/poretools/poretools_yield_plot.xml index 85a6e6ce47f..258a6ca5bf5 100644 --- a/tools/poretools/poretools_yield_plot.xml +++ b/tools/poretools/poretools_yield_plot.xml @@ -1,4 +1,3 @@ - of sequencing yield over time From fd0ed2a9d685ad4024cfa707bd4a34fc1545682d Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 26 Sep 2024 10:18:01 +0200 Subject: [PATCH 09/36] remove redundant options --- tools/poretools/.lint_skip | 2 -- tools/poretools/poretools_qualpos.xml | 6 +----- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/tools/poretools/.lint_skip b/tools/poretools/.lint_skip index 37306aaf5f8..033921a8a35 100644 --- a/tools/poretools/.lint_skip +++ b/tools/poretools/.lint_skip @@ -1,7 +1,5 @@ InputsNameDuplicate InputsNameRedundantArgument -InputsSelectOptionDuplicateText -InputsSelectOptionDuplicateValue TestsParamInInputs ToolVersionPEP404 XMLOrder diff --git a/tools/poretools/poretools_qualpos.xml b/tools/poretools/poretools_qualpos.xml index da4197542d2..28f955ae79a 100644 --- a/tools/poretools/poretools_qualpos.xml +++ b/tools/poretools/poretools_qualpos.xml @@ -1,4 +1,3 @@ - plot of quality score distribution over positions in nanopore reads @@ -14,10 +13,7 @@ poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length - - - - + From ee4f66c602b458badbbd84e1fb11ea385f847da9 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 10:22:52 +0200 Subject: [PATCH 10/36] add docstrings to all functions --- tools/idr_download/idr_download_by_ids.py | 119 ++++++++++++++++++++++ 1 file changed, 119 insertions(+) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index d4d0004b16a..84017a2f183 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -16,6 +16,15 @@ def warn(message, image_identifier, warn_skip=False): + """Print an error message to stderr and + - prefix with the image identifier + - suffix with 'Skipping download!' if warn_skip is True + + Args: + message (string): Message to print to stderr + image_identifier (string): Image identifier + warn_skip (bool, optional): Whether 'skipping download' should be suffix to the message. Defaults to False. + """ message = message.rstrip() if warn_skip: if message[-1] in [".", "!", "?"]: @@ -31,6 +40,15 @@ def warn(message, image_identifier, warn_skip=False): def find_channel_index(image, channel_name): + """Identify the channel index from the image and the channel name + + Args: + image (omero.gateway._ImageWrapper): image wrapper on which the channel should be identified + channel_name (string): name of the channel to look for + + Returns: + int: Index of the channel or -1 if was not found. + """ channel_name = channel_name.lower() for n, channel in enumerate(image.getChannelLabels()): if channel_name == channel.lower(): @@ -49,6 +67,22 @@ def find_channel_index(image, channel_name): def get_clipping_region(image, x, y, w, h): + """Check x,y and adjust w,h to image size to be able to crop the image with these coordinates + + Args: + image (omero.gateway._ImageWrapper): image wrapper on which region want to be cropped + x (int): left x coordinate + y (int): top y coordinate + w (int): width + h (int): height + + Raises: + ValueError: if the x or y coordinates are negative. + ValueError: if the x or y coordinates are larger than the width or height of the image. + + Returns: + list of int: new x, y, width, height adjusted to the image + """ # If the (x, y) coordinate falls outside the image boundaries, we # cannot just shift it because that would render the meaning of # w and h undefined (should width and height be decreased or the whole @@ -76,6 +110,15 @@ def get_clipping_region(image, x, y, w, h): def confine_plane(image, z): + """Adjust/Confine z to be among the possible z for the image + + Args: + image (omero.gateway._ImageWrapper): image wrapper for which the z is adjusted + z (int): plane index that need to be confined + + Returns: + int: confined z + """ if z < 0: z = 0 else: @@ -86,6 +129,15 @@ def confine_plane(image, z): def confine_frame(image, t): + """Adjust/Confine t to be among the possible t for the image + + Args: + image (omero.gateway._ImageWrapper): image wrapper for which the t is adjusted + t (int): frame index that need to be confined + + Returns: + int: confined t + """ if t < 0: t = 0 else: @@ -96,6 +148,18 @@ def confine_frame(image, t): def get_image_array(image, tile, z, c, t): + """Get a 2D numpy array from an image wrapper for a given tile, z, c, t + + Args: + image (omero.gateway._ImageWrapper): image wrapper from which values are taken + tile (list of int): [x, y, width, height] where x,y is the top left coordinate of the region to crop + z (int): plane index + c (int): channel index + t (int): frame index + + Returns: + numpy array of 2 dimensions: image values of the selected area + """ pixels = image.getPrimaryPixels() try: selection = pixels.getTile(theZ=z, theT=t, theC=c, tile=tile) @@ -108,13 +172,24 @@ def get_image_array(image, tile, z, c, t): def get_full_image_array(image): + """Get a 5D numpy array with all values from an image wrapper + + Args: + image (omero.gateway._ImageWrapper): image wrapper from which values are taken + + Returns: + numpy array of 5 dimensions: image values in the TZCYX order + """ # The goal is to get the image in TZCYX order pixels = image.getPrimaryPixels() + # Get the final tzclist in the order that will make the numpy reshape work tzclist = list( product( range(image.getSizeT()), range(image.getSizeZ()), range(image.getSizeC()) ) ) + # As getPlanes requires the indices in the zct order + # We keep the final order but switch indices zctlist = [(z, c, t) for (t, z, c) in tzclist] try: all_planes = numpy.array(list(pixels.getPlanes(zctlist))) @@ -152,6 +227,39 @@ def download_image_data( omero_secured=False, config_file=None, ): + """Download the image data of + either a list of image ids or all images from a dataset. + The image data can be: + - a 2D cropped region or + - a hyperstack written in a tiff file + - the original image uploaded in omero + Optionally, th final file can be in a tar + + Args: + image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-' + dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False. + download_original (bool, optional): Whether the original file uploded to omero should be downloaded. Defaults to False. + download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False. + channel (string, optional): Channel name. Defaults to None. + z_stack (int, optional): Z stack (plane) index. Defaults to 0. + frame (int, optional): T frame index. Defaults to 0. + coord (tuple of int, optional): Coordinates of the top left or center of the region to crop. Defaults to (0, 0). + width (int, optional): Width of the region to crop. Defaults to 0. + height (int, optional): Height of the region to crop. Defaults to 0. + region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center). Defaults to "rectangle". + skip_failed (bool, optional): Do not stop the downloads if one fails. Defaults to False. + download_tar (bool, optional): Put all downloaded images into a tar file. Defaults to False. + omero_host (str, optional): omero host url. Defaults to "idr.openmicroscopy.org". + omero_secured (bool, optional): Whether the omero connects with secure connection. Defaults to False. + config_file (string, optional): File path with config file with credentials to connect to OMERO. Defaults to None. + + Raises: + ValueError: If the region_spec is not 'rectangle' nor 'center' and a cropped region is wanted. + ValueError: If there is no dataset with this number in OMERO + ValueError: If there is no image with this number in OMERO + Exception: If the command to download the original image fails + ValueError: If the channel name could not be identified + """ if config_file is None: # IDR connection omero_username = "public" @@ -443,6 +551,17 @@ def download_image_data( def _center_to_ul(center_x, center_y, width, height): + """Convert the center coordinates, width, height to upper left coordinates, width, height + + Args: + center_x (int): x coordinate of center + center_y (int): y coordinate of center + width (int): width + height (int): height + + Returns: + list of 4 int: x, y, width, height where x,y are the upper left coordinates + """ if width > 0: ext_x = (width - 1) // 2 ul_x = max([center_x - ext_x, 0]) From 8c871221141cf1aa277f278be63f5f9345a56503 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 26 Sep 2024 10:25:41 +0200 Subject: [PATCH 11/36] fix redundant argument name and one redundant parameter --- tools/poretools/.lint_skip | 2 -- tools/poretools/macros.xml | 8 ++++---- tools/poretools/poretools_hist.xml | 2 +- tools/poretools/poretools_occupancy.xml | 2 +- tools/poretools/poretools_qualpos.xml | 3 +-- tools/poretools/poretools_squiggle.xml | 2 +- tools/poretools/poretools_yield_plot.xml | 2 +- 7 files changed, 9 insertions(+), 12 deletions(-) diff --git a/tools/poretools/.lint_skip b/tools/poretools/.lint_skip index 033921a8a35..82f678123db 100644 --- a/tools/poretools/.lint_skip +++ b/tools/poretools/.lint_skip @@ -1,5 +1,3 @@ -InputsNameDuplicate -InputsNameRedundantArgument TestsParamInInputs ToolVersionPEP404 XMLOrder diff --git a/tools/poretools/macros.xml b/tools/poretools/macros.xml index 5efbdd0212d..3d901ebc11c 100644 --- a/tools/poretools/macros.xml +++ b/tools/poretools/macros.xml @@ -24,7 +24,7 @@ - + @@ -36,7 +36,7 @@ - + @@ -49,8 +49,8 @@ - - + + 18.09 diff --git a/tools/poretools/poretools_hist.xml b/tools/poretools/poretools_hist.xml index 49c37aafa72..d5bde96ac84 100644 --- a/tools/poretools/poretools_hist.xml +++ b/tools/poretools/poretools_hist.xml @@ -15,7 +15,7 @@ poretools hist '$input' --saveas histogram.$extension --min-length $min_length - - + diff --git a/tools/poretools/poretools_occupancy.xml b/tools/poretools/poretools_occupancy.xml index 70300d62e2f..c8d3461a2bf 100644 --- a/tools/poretools/poretools_occupancy.xml +++ b/tools/poretools/poretools_occupancy.xml @@ -23,7 +23,7 @@ mv occupancy.$extension '$output' - + diff --git a/tools/poretools/poretools_qualpos.xml b/tools/poretools/poretools_qualpos.xml index 28f955ae79a..05d555dfec8 100644 --- a/tools/poretools/poretools_qualpos.xml +++ b/tools/poretools/poretools_qualpos.xml @@ -14,9 +14,8 @@ poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length - - + diff --git a/tools/poretools/poretools_squiggle.xml b/tools/poretools/poretools_squiggle.xml index dd16e052860..d23cd5a0008 100644 --- a/tools/poretools/poretools_squiggle.xml +++ b/tools/poretools/poretools_squiggle.xml @@ -14,7 +14,7 @@ poretools squiggle '$input' --saveas $extension --num-facets $num_facets $theme_ - + diff --git a/tools/poretools/poretools_yield_plot.xml b/tools/poretools/poretools_yield_plot.xml index 258a6ca5bf5..e2dbb66f5e2 100644 --- a/tools/poretools/poretools_yield_plot.xml +++ b/tools/poretools/poretools_yield_plot.xml @@ -18,7 +18,7 @@ poretools yield_plot '$input' --saveas plot.$extension --plot-type $plot_type - + From 5d732aba34d47d0664d8e64b90cf4fdf8c4f2c2d Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 26 Sep 2024 10:28:28 +0200 Subject: [PATCH 12/36] fix XMLOrder --- tools/poretools/.lint_skip | 1 - tools/poretools/poretools_events.xml | 2 +- tools/poretools/poretools_extract.xml | 2 +- tools/poretools/poretools_hist.xml | 2 +- tools/poretools/poretools_nucdist.xml | 2 +- tools/poretools/poretools_occupancy.xml | 2 +- tools/poretools/poretools_qualdist.xml | 2 +- tools/poretools/poretools_qualpos.xml | 2 +- tools/poretools/poretools_squiggle.xml | 2 +- tools/poretools/poretools_stats.xml | 2 +- tools/poretools/poretools_tabular.xml | 2 +- tools/poretools/poretools_times.xml | 2 +- tools/poretools/poretools_winner.xml | 2 +- tools/poretools/poretools_yield_plot.xml | 2 +- 14 files changed, 13 insertions(+), 14 deletions(-) diff --git a/tools/poretools/.lint_skip b/tools/poretools/.lint_skip index 82f678123db..3c8f09ef4e9 100644 --- a/tools/poretools/.lint_skip +++ b/tools/poretools/.lint_skip @@ -1,3 +1,2 @@ TestsParamInInputs ToolVersionPEP404 -XMLOrder diff --git a/tools/poretools/poretools_events.xml b/tools/poretools/poretools_events.xml index 50ad5aab59c..0cd5969bf24 100644 --- a/tools/poretools/poretools_events.xml +++ b/tools/poretools/poretools_events.xml @@ -1,9 +1,9 @@ from a set of sequencing reads - macros.xml + in FASTA or FASTQ format from nanopore files - macros.xml + of nanopore read lengths - macros.xml + distribution in nanopore sequencing reads - macros.xml + per cell in nanopore reads - macros.xml + score distribution in nanopore sequencing reads - macros.xml + plot of quality score distribution over positions in nanopore reads - macros.xml + for nanopore reads - macros.xml + from a set of FAST5 files - macros.xml + in tabular format from a set of FAST5 files - macros.xml + and channel information from a set of FAST5 files - macros.xml + from a set of FAST5 files. - macros.xml + of sequencing yield over time - macros.xml + Date: Thu, 26 Sep 2024 10:48:55 +0200 Subject: [PATCH 13/36] clarify the mutually exclusion of rectangle/center/download_full/download_original and the fact that channel/frame/z_stack are ignored if download_full or download_orignal is used. --- tools/idr_download/idr_download_by_ids.py | 73 ++++++++++++++--------- 1 file changed, 44 insertions(+), 29 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 84017a2f183..bde548ac799 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -238,15 +238,15 @@ def download_image_data( Args: image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-' dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False. - download_original (bool, optional): Whether the original file uploded to omero should be downloaded. Defaults to False. + download_original (bool, optional): Whether the original file uploded to omero should be downloaded (ignored if `download_full` is set to True). Defaults to False. download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False. - channel (string, optional): Channel name. Defaults to None. - z_stack (int, optional): Z stack (plane) index. Defaults to 0. - frame (int, optional): T frame index. Defaults to 0. - coord (tuple of int, optional): Coordinates of the top left or center of the region to crop. Defaults to (0, 0). - width (int, optional): Width of the region to crop. Defaults to 0. - height (int, optional): Height of the region to crop. Defaults to 0. - region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center). Defaults to "rectangle". + channel (string, optional): Channel name (ignored if `download_full` or `download_original` is set to True). Defaults to None. + z_stack (int, optional): Z stack (plane) index (ignored if `download_full` or `download_original` is set to True). Defaults to 0. + frame (int, optional): T frame index (ignored if `download_full` or `download_original` is set to True). Defaults to 0. + coord (tuple of int, optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0). + width (int, optional): Width of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0. + height (int, optional): Height of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0. + region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center, ignored if `download_full` or `download_original` is set to True). Defaults to "rectangle". skip_failed (bool, optional): Do not stop the downloads if one fails. Defaults to False. download_tar (bool, optional): Put all downloaded images into a tar file. Defaults to False. omero_host (str, optional): omero host url. Defaults to "idr.openmicroscopy.org". @@ -587,25 +587,6 @@ def _center_to_ul(center_x, center_y, width, height): "for which to retrieve data (default: " "read ids from stdin).", ) - p.add_argument( - "--download-original", - dest="download_original", - action="store_true", - help="download the original file uploaded to omero", - ) - p.add_argument( - "--download-full", - dest="download_full", - action="store_true", - help="download the full image on omero", - ) - p.add_argument( - "-c", - "--channel", - help="name of the channel to retrieve data for " - "(note: the first channel of each image will be downloaded if " - "left unspecified)", - ) region = p.add_mutually_exclusive_group() region.add_argument( "--rectangle", @@ -629,8 +610,42 @@ def _center_to_ul(center_x, center_y, width, height): "Note: Even values for width and height will be rounded down to " "the nearest odd number.", ) - p.add_argument("-f", "--frame", type=int, default=0) - p.add_argument("-z", "--z-stack", type=int, default=0) + region.add_argument( + "--download-original", + dest="download_original", + action="store_true", + help="download the original file uploaded to omero", + ) + region.add_argument( + "--download-full", + dest="download_full", + action="store_true", + help="download the full image on omero", + ) + p.add_argument( + "-c", + "--channel", + help="name of the channel to retrieve data for " + "(note: the first channel of each image will be downloaded if " + "left unspecified), ignored with `--download-original` and " + "`--download-full`", + ) + p.add_argument( + "-f", + "--frame", + type=int, + default=0, + help="index of the frame to retrive data for (first frame is 0)," + " ignored with `--download-original` and `--download-full`", + ) + p.add_argument( + "-z", + "--z-stack", + type=int, + default=0, + help="index of the slice to retrive data for (first slice is 0)," + " ignored with `--download-original` and `--download-full`", + ) p.add_argument("--skip-failed", action="store_true") p.add_argument("--download-tar", action="store_true") p.add_argument("-oh", "--omero-host", type=str, default="idr.openmicroscopy.org") From c463311a8056f1adeb6599a4a44d4236981096fc Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 10:51:46 +0200 Subject: [PATCH 14/36] remove libtiff dependency --- tools/idr_download/idr_download_by_ids.py | 7 +------ tools/idr_download/idr_download_by_ids.xml | 1 - 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index bde548ac799..bd7d42e6264 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -8,7 +8,6 @@ from tempfile import TemporaryDirectory import numpy -from libtiff import TIFF from omero.cli import cli_login from omero.constants.namespaces import NSBULKANNOTATIONS from omero.gateway import BlitzGateway @@ -532,11 +531,7 @@ def download_image_data( if download_tar: fname = os.path.join(tempdir, fname) - try: - tiff = TIFF.open(fname, mode="w") - tiff.write_image(im_array) - finally: - tiff.close() + imwrite(fname, im_array) # move image into tarball if download_tar: archive.add(fname, os.path.basename(fname)) diff --git a/tools/idr_download/idr_download_by_ids.xml b/tools/idr_download/idr_download_by_ids.xml index a56d4f9684d..31fe96c3514 100644 --- a/tools/idr_download/idr_download_by_ids.xml +++ b/tools/idr_download/idr_download_by_ids.xml @@ -20,7 +20,6 @@ omero-py - pylibtiff tifffile Date: Thu, 26 Sep 2024 13:06:16 +0200 Subject: [PATCH 15/36] fix wrong test parameters --- tools/poretools/.lint_skip | 1 - tools/poretools/poretools_tabular.xml | 15 ++++------- tools/poretools/poretools_times.xml | 26 ------------------- tools/poretools/poretools_winner.xml | 8 +++--- .../test-data/poretools-tabular-out1.tabular | 8 ------ .../test-data/poretools-tabular-out2.tabular | 8 ------ .../test-data/poretools-tabular-out3.tabular | 8 ------ .../test-data/poretools-tabular-out4.tabular | 8 ------ .../test-data/poretools-times-out2.tabular | 5 ---- .../test-data/poretools-times-out3.tabular | 5 ---- .../test-data/poretools-times-out4.tabular | 5 ---- .../test-data/poretools-times-out5.tabular | 5 ---- .../test-data/poretools-winner-out1.tabular | 4 +-- .../test-data/poretools-winner-out2.tabular | 4 +-- 14 files changed, 13 insertions(+), 97 deletions(-) delete mode 100644 tools/poretools/test-data/poretools-times-out2.tabular delete mode 100644 tools/poretools/test-data/poretools-times-out3.tabular delete mode 100644 tools/poretools/test-data/poretools-times-out4.tabular delete mode 100644 tools/poretools/test-data/poretools-times-out5.tabular diff --git a/tools/poretools/.lint_skip b/tools/poretools/.lint_skip index 3c8f09ef4e9..d710671f533 100644 --- a/tools/poretools/.lint_skip +++ b/tools/poretools/.lint_skip @@ -1,2 +1 @@ -TestsParamInInputs ToolVersionPEP404 diff --git a/tools/poretools/poretools_tabular.xml b/tools/poretools/poretools_tabular.xml index d92dd37c808..912147fecf7 100644 --- a/tools/poretools/poretools_tabular.xml +++ b/tools/poretools/poretools_tabular.xml @@ -20,32 +20,27 @@ - - + - - + - - + - - + - - + diff --git a/tools/poretools/poretools_times.xml b/tools/poretools/poretools_times.xml index 44e84146653..7522d695467 100644 --- a/tools/poretools/poretools_times.xml +++ b/tools/poretools/poretools_times.xml @@ -19,34 +19,8 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - Collect read size statistics from a set of FAST5 files. diff --git a/tools/poretools/poretools_winner.xml b/tools/poretools/poretools_winner.xml index 63ad4e6cdfa..c27ba4c95bd 100644 --- a/tools/poretools/poretools_winner.xml +++ b/tools/poretools/poretools_winner.xml @@ -20,22 +20,22 @@ - + - + - + - + diff --git a/tools/poretools/test-data/poretools-tabular-out1.tabular b/tools/poretools/test-data/poretools-tabular-out1.tabular index 2690807f14b..75b3169e3f0 100644 --- a/tools/poretools/test-data/poretools-tabular-out1.tabular +++ b/tools/poretools/test-data/poretools-tabular-out1.tabular @@ -1,13 +1,5 @@ length name sequence quals -202 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 GAAATTGCTGGTTGCTCCCCGAGGGGCCTATAAACAATCGGATAAGGGTCTAAGTCAGGGCGAAAAAGATTTGGGGGCTCCTAATCTCCGATAATGAGTGCCGCAACATACGGATAGTACCTTTATGCGTAACCGCTCCATACGACAAATAATTATTTATATACGGTACCTACGGAACCAAAATTGACAAGTTCGTACTTTT )))))+*,,*,*--,-,..---./0..++++-/-//**)*)))*,,.///---**)))*))+/,//-.,00.--)***+*+))),)*)))+).*----.--**..,-,**,**,+++++,+*+*)**+,,,**((+,,+,))()**+,++,+**+--,)(((((()(((((()(())))+,//),+--.+(())(((()((( -159 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 ATCGACCATATTGGCTTTTTGGTTATCCTGGTCTACCTCTTGTTGTCTTGGTGGGTGCCAACAGCTATGCATCTGTTGCATCAATCGTGACGGGAAACGAGAGGACAATTTCCCGGGTTAAACATGCCGATTGTCAGCCGCGGGGGCTGGGGAGGTTCC ""$"#$$&%$(&$"#$,<0-+(-'%(#$%$&(&%$$$%'-,(0'$)%(&$"'"#"'"$#$"&#&$##&%$%'%&'00,&'%#$##$$&"####%$'#%(''$$"$"($/=,)''#$$'%%'$'$)$%&$%()''%%"%&%%%(*#(%"$&&(&##&)&$ 212 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 CTTCTGTTGTGGTGCTCTTGCTCCCCAGGGGCCTATAAACGTGCACATAGGGTCTAAGTCAGCGAAAAAGATTTGAGGCTCCCGTATAGATAATGGATCCCCTCAGCCCTAGCTGACCGTCATCCGTAACGCCTCCATACATAAATAATTATTTAGCTCTAGTACACCCAGGCGGATCGCTTCTGGTTTTATATTTCTTGATTACTGATGCA "#')-,;42;7<8544/22.**)-(*()*(')%%&''-*0..+)%%$"'%'*/'%%&$&$%&##$%%(%)%/4)&#&'#$#$#$*#$"#&$$#'&$#*$%&##(&"*%)%&$&&&**(&(%%(%%),-%&%')*/,,(((%$%'$##","#,2''#$$('('*()(+)''&*)%$'(%#&%4.01-17;2&&$'12'')"%)&#$#"$)&'# -413 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 GCTTCTTCTGCTTATATTGCTTAGAAGGAAATACGAGAGGAGAAAGAGTAGATGATGATAAAGGGTCGACTAATTATTTCCGAAGTTTGTTAAAGTCGAAATCGCTTCGAATTTGAAATTGTTGCTGACGCAAGTTAGCGATGCGCGATCCCAGGAGTATAGGGGTTGAAAACGGTTCCATTTGATAAGGTTTTCCATTAATGACGTCACGTTGTTTGGTATTTCCTTCTATTTTCTCCGAAGCGCCCCTCTCTCTCTCATCTCACGTCAGATTCAATTTTATTACAACAAATGTGAAAAGTGGGTTCGCAGAGGTCGCTTAAGCCATTTTCTTAGATACAGCTTGAAAACGAATCTACAGAACAAATCTCCTGCCATTACACTCAGAGTCATGACGGTCGTGTTTATAGAGT ))****-+.,,,++,,-,...-*++/,0.1,++,,..-0/)+-/,----,+,,,-,--,-+****+**+**+-.-.0500-.0-,,+*,.,,,,+-*+./.++,.////10+/,/03/10/.0..-*--./0001.--.++../////0--,./0//****.//..--).0-,-*,,+*)10,+-+++,,./+,+++*)+-++++**)))*))*)+*+,*,.0,.+,****,--)))*)()+(*))))))))**,,,,*))((*))**))(*++(+*-,-,())))**+-0-*****./,)****-0/..,-,,.--,-+,****-./680/--*)+000/.//-,/03/..0--.*,++*+*)**)*)*++++.//0/,++**+))*+++*)))**++-,-,3520...**) -376 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 ACTCTAACTCAGGCTGGTATCTGAGTGTAATGGCGCAGTTGTCTGTAGGGTCGTTCAAGCTGTATCAAGAAATGAGTAAGCGAAAACCTGCGAGCCGATTTTCGCTTTGTTTAGTAAGGTTAGTGACGTGAGGGTGAGAGAGAGAGAGAGCGTTCGGAGAAAATAGAAGGAGAACCCAAACAACGTGACGTCATTGATGAAAACCTTATCGGGAACCCGTTTCAACCCCTATACTCCTCGGCGCGTAGGCTAACTGCGTAGCAACATTCAATTCAGCAGTTTTCCTGTCAGCGACTTCGGAAGCTTAGTCAACAGTGTTTATCAGCTCCTCTTCCTCTCGTATTTCGTTCAAGCAATATAGCAGAGGCGCCTGTCC "$###$$$#%#$"###$'###$"&'.)*(*+,-)$%$&/&$1(*),&&%%('$1)%##%%))+((%#$+&*%&&%$%%'(*,--+()$+-+),#*'%')4:*'$$*:,')'#%#%$&%$+++$*%$'&&)&&&&')'+*-,+*'&*$)%'&&'')'*)+,--'&&'$)(2&$)%%&(&&$&%#%%)$%&&((*(+$')(&(%##'+,+,)'((%%$%(*02*')&))+'"%$%%&'$#&%$$(#$&$%%##'&&,*))*((&%#(%*,(*(**$'()%#*=?/-&*)*(##&%'&+,(+*,)%'&*+*+('%($#'#*2+('%$$$&&%#$(+(('''(')'+30,$)*'((*('&&%#$$%%&%''$'$%&&1/$ 373 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 CATTCTTTGGTGCTGATCCTGCGAGGAGAGGGGGAGGGGAACAATGGTAGCCACTAAATCTATAACAATTATTTCAGAAGTTGTCCGCTTGAATCATTCATTTGAAATTGTTAGTGACGCAAGTTAATGCGCGATCCCAGGAGCGGGCTCGTCCAGTTTACAATTGTCCATGCGTAGTCAGTTGTTATGTTGATTCCTGTTACCGATAGGGTATATAACGCTCCTAGTCGATTCGATTTGCTTGGCGCCATCCAAGTATTCCAGAGTCCTTAGCATTTTCTTAATGGCACGTGAAAACGAATCCCCTAAGAGCCACTTATCACGTCCGATTACATACTCCAGTCATGACGCTTCTGTTTATGTTTCTTAACCA ##''$%)0%%)$&''',&'(&&$-+*-'('*+(('$$&#'#$%$%##$$#%$$#"$%$'$##$%"%#%)&$,5+($),,*0(&,####&)()(**)+)&$&,$&%1,3-*.''#'#$'('/*)+&&&+$&'%()*((%%)$&$#####"$%3%)')5/($$##&*$0%&()#$%%$$&'%(+%&-)%&%,-##((%$%&)*%&&#%""####"#"$$##""#('#$''$$&)0(&(.//$$&&###%&&+%('&%##%+)&&'%$#&%#%$#"(%/FA/+,(&'##$&%%#(&%*1)*()'())*("#$$(%%(&%*%$$$"$#($%##+$$%$####%$'&((&&$$%$)'1.+*:7,))',7&%)#$#$$# -523 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 ATGTTTCTTCAGTGATACCTGTGACATCCGGAAAGGAGGAGGAGGATCAGAAAGGAGGAGTGTGACATAACGCTGACAGTGCGTGCTTAGGTTCGTTAATAAACAAAGCCATATTACGGAGATGGCGTAATCACCTACGATGAAAGTGGTCACGTACGCGTGCCACCTGGGCATCGTCCTCACCCCTTCATTAAATTACAGGCTTTTGACTCCTTCAACCTTCTCGTTGTAATTGGTTAGTACTTATCCTATCTTATTCGCGATCGGCGTTCGATTGGATTTCGCTTCGAATGTAATCCGTATGCGCAATACAAATATTTGAGCTAATTTCCTCTCTTTACGTAATCGTTTTCGTCACCGTCGTCAATTATCGATACGGGAATCAAGTCGAACGAACCCCTGACCGAGAATCAGAAAAACTTTCAGAAGAAAAAGGAAGAAGAGAAAGCTCTTTCACATTGTAAACCAAACGCGAAAGCTCCCGAAAACAAAGGGCGGCGATTCTAAACATTTGGTTTATGTT (((*-,+,,,++*()(())*-)),....+/-,.),-++--./-,))*()))+*+*)*-*,**)())((*)(*()(*--+**)()()*(())))*,--*,+,.,---+)+))()**((())*+,-/./,--,++****+,+,,-02.///..-.--...,,))))))*++,+*++,+++*)*++-+*+**)+++**+)))(((())+*()((()(()))))))((((),-./--+*)))((((()((((((*+,,+,*+*,++++****,1.+*++,+,-.2-,+,-,+*,*.-.1/----*+,*+**++***./.-+*-+))))*,,-/*-*****-,*))))**,+++-,++++*+*,-../.-,**)*)+******-+,+)*++*+-.//../..,,+,..+.)+-+,))*+*++,+*,----.//-0662.-,--.-0.../.,+))-,2/.-++*****+**++++-+-...+,+*****,,.,+*.+,,,++*)))+/.,-10,+***)**++***+* -464 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 GAACACAACTGTTTCCCAGTACACGCTTTGTTTAAGCTTTCGCGTTGGTTCCATGTGAAGAGCTTCTGTTCTTCCTTTTTTGGTATGAAAGTTTTAGTTCTCTTCAGAGTCGTCCCACTTGATGTCCCGTATCGCTTGTGGACATTGTAGAAATGATCGTAAGGGCAGAGGAATTAATTAAAACTTTGTGGTGCCATCCCATTACGGTCGAGCGAATCCAGTAGCACCAGTACCCAGTAAGAACGAACCCTGAGCCAATTACACAGAAGGTTGAAGGAGTCAAGCTGTAGTTGGAAGGGGTGAAGGTCCGCACAAGATTCGATCCTCGTTATCGTACCTGATTACACATCTCTGCGTGATATGATGATTCTTTATTAGCAACCGAGCACGCACTGTTGGCGTTATGTTCGGATACTACGGTCTATCCTCTCAAACGGTCCAGCTCCCAACATCGGCGTCAGTCA #"#$"$%%#$#*3.$%&%$(#$%#$#'-,(4*$#$$%(2+'&%%*.%%,:'%&,)*,'%(%%$*,'''(*(%,'%)2>B>/'#$$&&$)+%/;,&#$()'&'&&($%#$(&&*&$$$#%%$$'&)+%&$)#%$##%'%&%#$$#&-%##&$&$#$#%$$$%&##&$$$&,-('(###'$')'#$+14(&$$($%$%#$&#'*+)*%)+$$&%$'&&(%&&%)"%$$'&%#)#%'#'$'%'(%&%%&%&%#$###&#&'+&####$($$$#'*)(+,-*$)&&'$&%$$$$((%+'&&$%#''$$$#&$%%$#$$$,%(*&"#&###(&*$%%%$&#$$%$&)+()$(&'$%$$##$)"&$#$##$&#&.#&1)&(%%'%&#'%#&&&%$&%$%(',('('&)+&%%-&#"$#%$%$$'$$,)(),'%%$$$###'##*((%(%%'%#$##"%##$(*-)&'&%# 494 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 TTGTGTTTCTTCTTATGACTTGCTATGCGCAGGGGGGAGGAGAGATGTAGCGGAGGGCAGAGTGTGAAAGGGGTAGTTCATTATGCTGTCGTTAAGCCTCCGGGGCTATTGAAAACGATGAATGGGGCCAGGCGCTGGTCACGTACACGTGCGACACTGATGAAACGTTCCTCACCATTCATTAAATTACCGGCTTTTAAACGTGAACATGCTGTTGTAATTCTTCATGGTGGTGTAATGTACTTAGCAGTAGCGTTCAATTGGATTTCGCTTCGAATGTAGTCGATCTGCGCATCCACTGGTCGACGATTTCCTCTCTTTACTGATCGTAGTTCGTCACGTCGTCGTACGATAGGATCAAAGTCGCGGGATGGCTATCCCCGGGCGAACTTTCCAGAGAAGGAAGAAGAAAGACCTTTCGGCTTGTAGTAAGACCCCGAAGACTCGAAAACAGGGCAACGCGAATTCCACTTCGTTATGTTCTTACTATTGGA #$$*)*8+$()&(%%$#$#&'$#"%%#$($+&,&(-(',.,*%$%%$$$"$$('%%'&('%%%%%$##$#$$"$#$%&%$&$#'$$#$)''+&$%"&##($#$$###$*&*$&(%%$&($&$&"###%$$#&"#!%$$($$%$'$&%&'*%&$#$#$%$$$($/$/.2)'$#%#%(#**)%)&'$#)%#%''(%')0'$%#$$'$&#$#&$&$&,2-,/%1,"%*%%$#%&##%%&)((('&%(&&%'*%&'$((-:'%(**)((/5)%$&,,*%)#'%$$#&$"#'$)$&%%%#$$%#$#"'$"#$"$17)&##%&')3'##$$$$$#%#%+)'&)&#+*,)&'%%&#%#%#$*%&%$%%##&&#%%'#'#$$%##$%)$'%%'%#'$#)48$$#%#'#*)-,,))')((%#$#&&-'(##'%*%$&"""$#$#')%$'($$#"'$&&)$&'%(*&%%'$$)+)6*(#%#%'%&*,)(&3*$%'$%%$(,,&# -692 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 CATGTTTCTGCTGATATTGCTAATGGCTGAACTGGAAATAAGGATCCGTTGCTTGCCAACAACTATACTGCGTGGTATTTTCCCAGTGGAAAGATCGGGAACCTTTGATCTTCAATATAGTTACAATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTTGGGTATAACAGGATGAGGAGGACGATTCGAAGTCACGATCATGCGCCCAAGTCAGAATGACTCCACACTACTCCTCCTCAGGACCATTTATAAATAAACAGTGATCAAGATTCCAACAATTAAGATGGCTTGAAACCAATTTCTGCTCTTGTTTTTGTTCCCACTCCCCCCTCCCCCCGAGGTCAGGATGAAGTATTAACTCTGAAGATAAAGGACCCCACGACGACAACGGCTTCCAGTTACTTCGAAGGCATTTTTCTACTTCTACTTCCCCTCCGTCTCATCCTCCTCCTCAGCTACCAAATTCACAATAGGACCGCAGGAAAAGTCTGTAGCGAATAGAACCTTCTTCACTACGGTTTCGTACCTAAAATGTTCTGGAAAAATGGATAGAAAAGAATCTTTTAAAATCGAAATCCGATTTTCGGAGTGTTAACAATGTAACTGTTGTAGAAAAGGAGCGGTAAATGAGACGTGGGGAATAAGATACAGAGCAACCACTGTCGTTAAGGACCGTTTGAGTGTTT ))))+-*)*)+**++**+)*)*,-,,+++-+++/./20.//.+...*.,-,--+***,+++++**+++,.//.,++,.54.320/--.,-.++-.,,.-++++*,+,-./0/.0000/..0-,----/.----,+++++,00.//./.++*+//0.//00/285/+*+**+-,,,,,-,**,,,+--00*0/)*.,+,+.,,,+++,,-+*,*+-+,+,--..,+****)**+++,+++***)*+)**)-,.20//02-))**++*+**+*+**-/0./-,,,--))*))++)+*++..,,+-./.+++++,++++,025-,5.-/,-//0/---,,.43430,,-+,+,.,/..-.+***)))))..//-+,***)))+)++))),***)**))(())--.-())((,((*(*(((*+-0/---,*/**)*,-/.0.-,.,++)*,+,,-,--,-,+++**))**,+*+*))))*))))*))+(+,-+,**)))*)*)))*++((*+****,,,---+*,+*+,0,++*)))(,03.--1+***-*-)*)+****))))+))+***+21--/.-)))**)*)***-10--,-,,+*+)))+,..,,/,,,,-,+)())***)())*++++,+)))***+*))((,+(((())(*)()()***,,---,,,+)((((,()**.*(***+))) -602 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 ACACTAGCATCTGTCTGGCCCCGATATTTGTAGTATGTACTTTACGTGTACTGTTACTATGGTATTTTCACCCTCAGTTTGCCCTTGTCACTCGAAAGTCGAATTCAGTGTTTTAAAAGATTGTCTGGTTCTATCGGTTCCGAGCAGTTTTAATAGAACTGATCAATGAAGAAGGTTCGTTCGAGCGAACTTCCAGTGATCTTGTGAATTTGAGCTGAGGAGGAGATGAAAGAGGGAAGTAGAAGTAGAAAAATTGCATCGAAATATGGAATAAATTGTATCGTCGGTCTTGCTTTTATCTGTCAGTTATACTTCAGTAGGAGGGAGTGGGATAACGACAGCAATTAGTTCAGCCTTAGTGTTGAGGAATCTGGTTCTTTAACATCTTTGGTGGGAGGAGTGTCCTTGATTTAATATGCAGAAGTATCCTTGCTGCGAATCGTCATCATCCTTTAACAATAGGATGAAAACCGTTAAAATGCCGACAGTTGGACCTGCGAGCCGCCGGCCCGTATTCATGGGAAAGTACCGCATTAACGTGTGTCAGGCGGGACGTATTATTTCCCGTTCAGCCGATTAAGTATACAGGCACAGAGACTTCC ####"##&%##$#+%%##%#'%#$%$)-)'($%&&((,()+-'&'(($%#(&%1-$##$'$#%#'08+'$$%#"&$#&.+$%*#('%%##$$&&)))$(''($(('##+)6<4)'(*()',,(.'&%&'*($%&%##-,('#$$"$$'04)&%$#('&%%%%'$##(%%$*$'$#'''&),%$%$%$%$$$*+%$%(%%&&''%%(&%1-(%$"#%&&+**-,'&''((&#'#$&%'&%'#(&+#)*))//+&&%$%$%$%&)&&$),-*&%$$$&)%$#$'&+(#%'&''$##(2(%&$%$..('($&%%*.+'$%%%),')'()%*'&)%#&##"###&%%%'*$'++($$%#'%%"($)&#$%''&(**)$+*&)3-&%$$$#$)&$%'%)*')&&$%%&$#&($#+0&$"##%###'%(%'&(%$%(%#&$%$&$&$#%###$$&$%&+&&$$%&$$'('&(&&&#%$$'%%&'%'"%###$$#-)%#$#%'%%$&'''"&%$$'%$$)#(-*&)+09))'#'#%&%&$$(&%%%)(+()&%$('"""$"#&#'$$'./(*&&('%$#$$##'%$&$&%$"&"))##$#'$##"$)'$ 657 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 GTATTTCTTATGATATTAGATGTAGGCTGGAAATAGAATGCGTGCTTTACAGGCCTCCTCTGCGTATGTTTCCATGGAAGCCGTAGGAACCTTTGATCTTCATACTTGCCCTATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTGATATAACAGGATACGGAAAGAGTTCGAAGTCGAATCGTCCAGCAAGTCGAATGACTCTAAAGACATCGGCACGGCCTTTGAGGCTCGTATATGCCTAATTCCAACAATGCAAAGTACGTGGAACAGATTTCTGCTCTTTTTTGTTCCACTCCGCCAGCCCCCCGAGGTCAGGATGAAATATTACTCTGAAAACCGCCAACCCACGGGACAGCTACGTCGAATGTCGTCGAACAGTTCTATTCCTTCCCCTCCGTTAGTACTACTCTAGGCTACTCAATTCAGGCGATAGAAGGAAAAGTCTGTACCAGGCGGGTTCTTCGGCTTTTCAATGCGCGCTGTTCTGGGGAGCTATCGCTGCAAAGAATCTTTTAAAATCGAGTCGAGTTTTCAGAGTGTTCCTCAATGTAACTGTTGGCAAAGGAGCGGGCCTGGCAGACGTGGGGAATAAGACCCCAAAACCACTTCGTGCACATCGTTCTGGTGTTCATCTGTTCTTAGCTCTTGT "##)7.'-(&&$$&#'$$$''%$%$&(),210)&&)&)+&.-+'((,%#))())&%)(')+)*+.***CC/&'$'')(*###$&%)5)1')&./%%)%++)&%$%%.#''(#%*)+&&).*)'*%$+A/'&%+%)''-;+)-'++-1)9>0()((%&%&&(')%$%#+-/&'#%+3&**/&''&'%'%$($%&$'(&'(&)*++)('&'#$$#"#"#%'$&%#$#")$&.'#&$%$$$$($&#)#%$#%,10*)%$&$,)&'"%#"%$&%1&')&%%%'-A:10/,+(*0KLI,,I330,**.,$&$'&,7255.)+(%'&&+$,%%%'$$$&&%$$&''$*)$$%#%$&$'%#$$$#"##$$%$$(#*'#$&%#&$#$$$(%&%'1)'%$/,(')3+0-,,1*)0$##'#$%$&&(#$$##"#$#'&$,(&&#$%$&$$)&+,++**(%+'&&%$$$%"$"#%$,5')(''&',:M/($&,&($%$$((7,&%%--$&$##$%$$%))$+*',.--+-3/'$')%&##&$*($''-3E3)$)'&('&)#&&())+)))('(&/*))',-&0**('&%#$##$)#'&+,,(&&&%)'%%$%&&*+&%$%"#$$$%)(()%&"#&#)&1.+,**++-C$&$$&$4(%)$$##$#$&$% diff --git a/tools/poretools/test-data/poretools-tabular-out2.tabular b/tools/poretools/test-data/poretools-tabular-out2.tabular index 2690807f14b..b5f564900d7 100644 --- a/tools/poretools/test-data/poretools-tabular-out2.tabular +++ b/tools/poretools/test-data/poretools-tabular-out2.tabular @@ -1,13 +1,5 @@ length name sequence quals -202 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 GAAATTGCTGGTTGCTCCCCGAGGGGCCTATAAACAATCGGATAAGGGTCTAAGTCAGGGCGAAAAAGATTTGGGGGCTCCTAATCTCCGATAATGAGTGCCGCAACATACGGATAGTACCTTTATGCGTAACCGCTCCATACGACAAATAATTATTTATATACGGTACCTACGGAACCAAAATTGACAAGTTCGTACTTTT )))))+*,,*,*--,-,..---./0..++++-/-//**)*)))*,,.///---**)))*))+/,//-.,00.--)***+*+))),)*)))+).*----.--**..,-,**,**,+++++,+*+*)**+,,,**((+,,+,))()**+,++,+**+--,)(((((()(((((()(())))+,//),+--.+(())(((()((( 159 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 ATCGACCATATTGGCTTTTTGGTTATCCTGGTCTACCTCTTGTTGTCTTGGTGGGTGCCAACAGCTATGCATCTGTTGCATCAATCGTGACGGGAAACGAGAGGACAATTTCCCGGGTTAAACATGCCGATTGTCAGCCGCGGGGGCTGGGGAGGTTCC ""$"#$$&%$(&$"#$,<0-+(-'%(#$%$&(&%$$$%'-,(0'$)%(&$"'"#"'"$#$"&#&$##&%$%'%&'00,&'%#$##$$&"####%$'#%(''$$"$"($/=,)''#$$'%%'$'$)$%&$%()''%%"%&%%%(*#(%"$&&(&##&)&$ -212 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 CTTCTGTTGTGGTGCTCTTGCTCCCCAGGGGCCTATAAACGTGCACATAGGGTCTAAGTCAGCGAAAAAGATTTGAGGCTCCCGTATAGATAATGGATCCCCTCAGCCCTAGCTGACCGTCATCCGTAACGCCTCCATACATAAATAATTATTTAGCTCTAGTACACCCAGGCGGATCGCTTCTGGTTTTATATTTCTTGATTACTGATGCA "#')-,;42;7<8544/22.**)-(*()*(')%%&''-*0..+)%%$"'%'*/'%%&$&$%&##$%%(%)%/4)&#&'#$#$#$*#$"#&$$#'&$#*$%&##(&"*%)%&$&&&**(&(%%(%%),-%&%')*/,,(((%$%'$##","#,2''#$$('('*()(+)''&*)%$'(%#&%4.01-17;2&&$'12'')"%)&#$#"$)&'# -413 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 GCTTCTTCTGCTTATATTGCTTAGAAGGAAATACGAGAGGAGAAAGAGTAGATGATGATAAAGGGTCGACTAATTATTTCCGAAGTTTGTTAAAGTCGAAATCGCTTCGAATTTGAAATTGTTGCTGACGCAAGTTAGCGATGCGCGATCCCAGGAGTATAGGGGTTGAAAACGGTTCCATTTGATAAGGTTTTCCATTAATGACGTCACGTTGTTTGGTATTTCCTTCTATTTTCTCCGAAGCGCCCCTCTCTCTCTCATCTCACGTCAGATTCAATTTTATTACAACAAATGTGAAAAGTGGGTTCGCAGAGGTCGCTTAAGCCATTTTCTTAGATACAGCTTGAAAACGAATCTACAGAACAAATCTCCTGCCATTACACTCAGAGTCATGACGGTCGTGTTTATAGAGT ))****-+.,,,++,,-,...-*++/,0.1,++,,..-0/)+-/,----,+,,,-,--,-+****+**+**+-.-.0500-.0-,,+*,.,,,,+-*+./.++,.////10+/,/03/10/.0..-*--./0001.--.++../////0--,./0//****.//..--).0-,-*,,+*)10,+-+++,,./+,+++*)+-++++**)))*))*)+*+,*,.0,.+,****,--)))*)()+(*))))))))**,,,,*))((*))**))(*++(+*-,-,())))**+-0-*****./,)****-0/..,-,,.--,-+,****-./680/--*)+000/.//-,/03/..0--.*,++*+*)**)*)*++++.//0/,++**+))*+++*)))**++-,-,3520...**) 376 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 ACTCTAACTCAGGCTGGTATCTGAGTGTAATGGCGCAGTTGTCTGTAGGGTCGTTCAAGCTGTATCAAGAAATGAGTAAGCGAAAACCTGCGAGCCGATTTTCGCTTTGTTTAGTAAGGTTAGTGACGTGAGGGTGAGAGAGAGAGAGAGCGTTCGGAGAAAATAGAAGGAGAACCCAAACAACGTGACGTCATTGATGAAAACCTTATCGGGAACCCGTTTCAACCCCTATACTCCTCGGCGCGTAGGCTAACTGCGTAGCAACATTCAATTCAGCAGTTTTCCTGTCAGCGACTTCGGAAGCTTAGTCAACAGTGTTTATCAGCTCCTCTTCCTCTCGTATTTCGTTCAAGCAATATAGCAGAGGCGCCTGTCC "$###$$$#%#$"###$'###$"&'.)*(*+,-)$%$&/&$1(*),&&%%('$1)%##%%))+((%#$+&*%&&%$%%'(*,--+()$+-+),#*'%')4:*'$$*:,')'#%#%$&%$+++$*%$'&&)&&&&')'+*-,+*'&*$)%'&&'')'*)+,--'&&'$)(2&$)%%&(&&$&%#%%)$%&&((*(+$')(&(%##'+,+,)'((%%$%(*02*')&))+'"%$%%&'$#&%$$(#$&$%%##'&&,*))*((&%#(%*,(*(**$'()%#*=?/-&*)*(##&%'&+,(+*,)%'&*+*+('%($#'#*2+('%$$$&&%#$(+(('''(')'+30,$)*'((*('&&%#$$%%&%''$'$%&&1/$ -373 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 CATTCTTTGGTGCTGATCCTGCGAGGAGAGGGGGAGGGGAACAATGGTAGCCACTAAATCTATAACAATTATTTCAGAAGTTGTCCGCTTGAATCATTCATTTGAAATTGTTAGTGACGCAAGTTAATGCGCGATCCCAGGAGCGGGCTCGTCCAGTTTACAATTGTCCATGCGTAGTCAGTTGTTATGTTGATTCCTGTTACCGATAGGGTATATAACGCTCCTAGTCGATTCGATTTGCTTGGCGCCATCCAAGTATTCCAGAGTCCTTAGCATTTTCTTAATGGCACGTGAAAACGAATCCCCTAAGAGCCACTTATCACGTCCGATTACATACTCCAGTCATGACGCTTCTGTTTATGTTTCTTAACCA ##''$%)0%%)$&''',&'(&&$-+*-'('*+(('$$&#'#$%$%##$$#%$$#"$%$'$##$%"%#%)&$,5+($),,*0(&,####&)()(**)+)&$&,$&%1,3-*.''#'#$'('/*)+&&&+$&'%()*((%%)$&$#####"$%3%)')5/($$##&*$0%&()#$%%$$&'%(+%&-)%&%,-##((%$%&)*%&&#%""####"#"$$##""#('#$''$$&)0(&(.//$$&&###%&&+%('&%##%+)&&'%$#&%#%$#"(%/FA/+,(&'##$&%%#(&%*1)*()'())*("#$$(%%(&%*%$$$"$#($%##+$$%$####%$'&((&&$$%$)'1.+*:7,))',7&%)#$#$$# -523 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 ATGTTTCTTCAGTGATACCTGTGACATCCGGAAAGGAGGAGGAGGATCAGAAAGGAGGAGTGTGACATAACGCTGACAGTGCGTGCTTAGGTTCGTTAATAAACAAAGCCATATTACGGAGATGGCGTAATCACCTACGATGAAAGTGGTCACGTACGCGTGCCACCTGGGCATCGTCCTCACCCCTTCATTAAATTACAGGCTTTTGACTCCTTCAACCTTCTCGTTGTAATTGGTTAGTACTTATCCTATCTTATTCGCGATCGGCGTTCGATTGGATTTCGCTTCGAATGTAATCCGTATGCGCAATACAAATATTTGAGCTAATTTCCTCTCTTTACGTAATCGTTTTCGTCACCGTCGTCAATTATCGATACGGGAATCAAGTCGAACGAACCCCTGACCGAGAATCAGAAAAACTTTCAGAAGAAAAAGGAAGAAGAGAAAGCTCTTTCACATTGTAAACCAAACGCGAAAGCTCCCGAAAACAAAGGGCGGCGATTCTAAACATTTGGTTTATGTT (((*-,+,,,++*()(())*-)),....+/-,.),-++--./-,))*()))+*+*)*-*,**)())((*)(*()(*--+**)()()*(())))*,--*,+,.,---+)+))()**((())*+,-/./,--,++****+,+,,-02.///..-.--...,,))))))*++,+*++,+++*)*++-+*+**)+++**+)))(((())+*()((()(()))))))((((),-./--+*)))((((()((((((*+,,+,*+*,++++****,1.+*++,+,-.2-,+,-,+*,*.-.1/----*+,*+**++***./.-+*-+))))*,,-/*-*****-,*))))**,+++-,++++*+*,-../.-,**)*)+******-+,+)*++*+-.//../..,,+,..+.)+-+,))*+*++,+*,----.//-0662.-,--.-0.../.,+))-,2/.-++*****+**++++-+-...+,+*****,,.,+*.+,,,++*)))+/.,-10,+***)**++***+* 464 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 GAACACAACTGTTTCCCAGTACACGCTTTGTTTAAGCTTTCGCGTTGGTTCCATGTGAAGAGCTTCTGTTCTTCCTTTTTTGGTATGAAAGTTTTAGTTCTCTTCAGAGTCGTCCCACTTGATGTCCCGTATCGCTTGTGGACATTGTAGAAATGATCGTAAGGGCAGAGGAATTAATTAAAACTTTGTGGTGCCATCCCATTACGGTCGAGCGAATCCAGTAGCACCAGTACCCAGTAAGAACGAACCCTGAGCCAATTACACAGAAGGTTGAAGGAGTCAAGCTGTAGTTGGAAGGGGTGAAGGTCCGCACAAGATTCGATCCTCGTTATCGTACCTGATTACACATCTCTGCGTGATATGATGATTCTTTATTAGCAACCGAGCACGCACTGTTGGCGTTATGTTCGGATACTACGGTCTATCCTCTCAAACGGTCCAGCTCCCAACATCGGCGTCAGTCA #"#$"$%%#$#*3.$%&%$(#$%#$#'-,(4*$#$$%(2+'&%%*.%%,:'%&,)*,'%(%%$*,'''(*(%,'%)2>B>/'#$$&&$)+%/;,&#$()'&'&&($%#$(&&*&$$$#%%$$'&)+%&$)#%$##%'%&%#$$#&-%##&$&$#$#%$$$%&##&$$$&,-('(###'$')'#$+14(&$$($%$%#$&#'*+)*%)+$$&%$'&&(%&&%)"%$$'&%#)#%'#'$'%'(%&%%&%&%#$###&#&'+&####$($$$#'*)(+,-*$)&&'$&%$$$$((%+'&&$%#''$$$#&$%%$#$$$,%(*&"#&###(&*$%%%$&#$$%$&)+()$(&'$%$$##$)"&$#$##$&#&.#&1)&(%%'%&#'%#&&&%$&%$%(',('('&)+&%%-&#"$#%$%$$'$$,)(),'%%$$$###'##*((%(%%'%#$##"%##$(*-)&'&%# -494 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 TTGTGTTTCTTCTTATGACTTGCTATGCGCAGGGGGGAGGAGAGATGTAGCGGAGGGCAGAGTGTGAAAGGGGTAGTTCATTATGCTGTCGTTAAGCCTCCGGGGCTATTGAAAACGATGAATGGGGCCAGGCGCTGGTCACGTACACGTGCGACACTGATGAAACGTTCCTCACCATTCATTAAATTACCGGCTTTTAAACGTGAACATGCTGTTGTAATTCTTCATGGTGGTGTAATGTACTTAGCAGTAGCGTTCAATTGGATTTCGCTTCGAATGTAGTCGATCTGCGCATCCACTGGTCGACGATTTCCTCTCTTTACTGATCGTAGTTCGTCACGTCGTCGTACGATAGGATCAAAGTCGCGGGATGGCTATCCCCGGGCGAACTTTCCAGAGAAGGAAGAAGAAAGACCTTTCGGCTTGTAGTAAGACCCCGAAGACTCGAAAACAGGGCAACGCGAATTCCACTTCGTTATGTTCTTACTATTGGA #$$*)*8+$()&(%%$#$#&'$#"%%#$($+&,&(-(',.,*%$%%$$$"$$('%%'&('%%%%%$##$#$$"$#$%&%$&$#'$$#$)''+&$%"&##($#$$###$*&*$&(%%$&($&$&"###%$$#&"#!%$$($$%$'$&%&'*%&$#$#$%$$$($/$/.2)'$#%#%(#**)%)&'$#)%#%''(%')0'$%#$$'$&#$#&$&$&,2-,/%1,"%*%%$#%&##%%&)((('&%(&&%'*%&'$((-:'%(**)((/5)%$&,,*%)#'%$$#&$"#'$)$&%%%#$$%#$#"'$"#$"$17)&##%&')3'##$$$$$#%#%+)'&)&#+*,)&'%%&#%#%#$*%&%$%%##&&#%%'#'#$$%##$%)$'%%'%#'$#)48$$#%#'#*)-,,))')((%#$#&&-'(##'%*%$&"""$#$#')%$'($$#"'$&&)$&'%(*&%%'$$)+)6*(#%#%'%&*,)(&3*$%'$%%$(,,&# -692 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 CATGTTTCTGCTGATATTGCTAATGGCTGAACTGGAAATAAGGATCCGTTGCTTGCCAACAACTATACTGCGTGGTATTTTCCCAGTGGAAAGATCGGGAACCTTTGATCTTCAATATAGTTACAATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTTGGGTATAACAGGATGAGGAGGACGATTCGAAGTCACGATCATGCGCCCAAGTCAGAATGACTCCACACTACTCCTCCTCAGGACCATTTATAAATAAACAGTGATCAAGATTCCAACAATTAAGATGGCTTGAAACCAATTTCTGCTCTTGTTTTTGTTCCCACTCCCCCCTCCCCCCGAGGTCAGGATGAAGTATTAACTCTGAAGATAAAGGACCCCACGACGACAACGGCTTCCAGTTACTTCGAAGGCATTTTTCTACTTCTACTTCCCCTCCGTCTCATCCTCCTCCTCAGCTACCAAATTCACAATAGGACCGCAGGAAAAGTCTGTAGCGAATAGAACCTTCTTCACTACGGTTTCGTACCTAAAATGTTCTGGAAAAATGGATAGAAAAGAATCTTTTAAAATCGAAATCCGATTTTCGGAGTGTTAACAATGTAACTGTTGTAGAAAAGGAGCGGTAAATGAGACGTGGGGAATAAGATACAGAGCAACCACTGTCGTTAAGGACCGTTTGAGTGTTT ))))+-*)*)+**++**+)*)*,-,,+++-+++/./20.//.+...*.,-,--+***,+++++**+++,.//.,++,.54.320/--.,-.++-.,,.-++++*,+,-./0/.0000/..0-,----/.----,+++++,00.//./.++*+//0.//00/285/+*+**+-,,,,,-,**,,,+--00*0/)*.,+,+.,,,+++,,-+*,*+-+,+,--..,+****)**+++,+++***)*+)**)-,.20//02-))**++*+**+*+**-/0./-,,,--))*))++)+*++..,,+-./.+++++,++++,025-,5.-/,-//0/---,,.43430,,-+,+,.,/..-.+***)))))..//-+,***)))+)++))),***)**))(())--.-())((,((*(*(((*+-0/---,*/**)*,-/.0.-,.,++)*,+,,-,--,-,+++**))**,+*+*))))*))))*))+(+,-+,**)))*)*)))*++((*+****,,,---+*,+*+,0,++*)))(,03.--1+***-*-)*)+****))))+))+***+21--/.-)))**)*)***-10--,-,,+*+)))+,..,,/,,,,-,+)())***)())*++++,+)))***+*))((,+(((())(*)()()***,,---,,,+)((((,()**.*(***+))) 602 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 ACACTAGCATCTGTCTGGCCCCGATATTTGTAGTATGTACTTTACGTGTACTGTTACTATGGTATTTTCACCCTCAGTTTGCCCTTGTCACTCGAAAGTCGAATTCAGTGTTTTAAAAGATTGTCTGGTTCTATCGGTTCCGAGCAGTTTTAATAGAACTGATCAATGAAGAAGGTTCGTTCGAGCGAACTTCCAGTGATCTTGTGAATTTGAGCTGAGGAGGAGATGAAAGAGGGAAGTAGAAGTAGAAAAATTGCATCGAAATATGGAATAAATTGTATCGTCGGTCTTGCTTTTATCTGTCAGTTATACTTCAGTAGGAGGGAGTGGGATAACGACAGCAATTAGTTCAGCCTTAGTGTTGAGGAATCTGGTTCTTTAACATCTTTGGTGGGAGGAGTGTCCTTGATTTAATATGCAGAAGTATCCTTGCTGCGAATCGTCATCATCCTTTAACAATAGGATGAAAACCGTTAAAATGCCGACAGTTGGACCTGCGAGCCGCCGGCCCGTATTCATGGGAAAGTACCGCATTAACGTGTGTCAGGCGGGACGTATTATTTCCCGTTCAGCCGATTAAGTATACAGGCACAGAGACTTCC ####"##&%##$#+%%##%#'%#$%$)-)'($%&&((,()+-'&'(($%#(&%1-$##$'$#%#'08+'$$%#"&$#&.+$%*#('%%##$$&&)))$(''($(('##+)6<4)'(*()',,(.'&%&'*($%&%##-,('#$$"$$'04)&%$#('&%%%%'$##(%%$*$'$#'''&),%$%$%$%$$$*+%$%(%%&&''%%(&%1-(%$"#%&&+**-,'&''((&#'#$&%'&%'#(&+#)*))//+&&%$%$%$%&)&&$),-*&%$$$&)%$#$'&+(#%'&''$##(2(%&$%$..('($&%%*.+'$%%%),')'()%*'&)%#&##"###&%%%'*$'++($$%#'%%"($)&#$%''&(**)$+*&)3-&%$$$#$)&$%'%)*')&&$%%&$#&($#+0&$"##%###'%(%'&(%$%(%#&$%$&$&$#%###$$&$%&+&&$$%&$$'('&(&&&#%$$'%%&'%'"%###$$#-)%#$#%'%%$&'''"&%$$'%$$)#(-*&)+09))'#'#%&%&$$(&%%%)(+()&%$('"""$"#&#'$$'./(*&&('%$#$$##'%$&$&%$"&"))##$#'$##"$)'$ -657 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 GTATTTCTTATGATATTAGATGTAGGCTGGAAATAGAATGCGTGCTTTACAGGCCTCCTCTGCGTATGTTTCCATGGAAGCCGTAGGAACCTTTGATCTTCATACTTGCCCTATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTGATATAACAGGATACGGAAAGAGTTCGAAGTCGAATCGTCCAGCAAGTCGAATGACTCTAAAGACATCGGCACGGCCTTTGAGGCTCGTATATGCCTAATTCCAACAATGCAAAGTACGTGGAACAGATTTCTGCTCTTTTTTGTTCCACTCCGCCAGCCCCCCGAGGTCAGGATGAAATATTACTCTGAAAACCGCCAACCCACGGGACAGCTACGTCGAATGTCGTCGAACAGTTCTATTCCTTCCCCTCCGTTAGTACTACTCTAGGCTACTCAATTCAGGCGATAGAAGGAAAAGTCTGTACCAGGCGGGTTCTTCGGCTTTTCAATGCGCGCTGTTCTGGGGAGCTATCGCTGCAAAGAATCTTTTAAAATCGAGTCGAGTTTTCAGAGTGTTCCTCAATGTAACTGTTGGCAAAGGAGCGGGCCTGGCAGACGTGGGGAATAAGACCCCAAAACCACTTCGTGCACATCGTTCTGGTGTTCATCTGTTCTTAGCTCTTGT "##)7.'-(&&$$&#'$$$''%$%$&(),210)&&)&)+&.-+'((,%#))())&%)(')+)*+.***CC/&'$'')(*###$&%)5)1')&./%%)%++)&%$%%.#''(#%*)+&&).*)'*%$+A/'&%+%)''-;+)-'++-1)9>0()((%&%&&(')%$%#+-/&'#%+3&**/&''&'%'%$($%&$'(&'(&)*++)('&'#$$#"#"#%'$&%#$#")$&.'#&$%$$$$($&#)#%$#%,10*)%$&$,)&'"%#"%$&%1&')&%%%'-A:10/,+(*0KLI,,I330,**.,$&$'&,7255.)+(%'&&+$,%%%'$$$&&%$$&''$*)$$%#%$&$'%#$$$#"##$$%$$(#*'#$&%#&$#$$$(%&%'1)'%$/,(')3+0-,,1*)0$##'#$%$&&(#$$##"#$#'&$,(&&#$%$&$$)&+,++**(%+'&&%$$$%"$"#%$,5')(''&',:M/($&,&($%$$((7,&%%--$&$##$%$$%))$+*',.--+-3/'$')%&##&$*($''-3E3)$)'&('&)#&&())+)))('(&/*))',-&0**('&%#$##$)#'&+,,(&&&%)'%%$%&&*+&%$%"#$$$%)(()%&"#&#)&1.+,**++-C$&$$&$4(%)$$##$#$&$% diff --git a/tools/poretools/test-data/poretools-tabular-out3.tabular b/tools/poretools/test-data/poretools-tabular-out3.tabular index 2690807f14b..ce9fa1cfcb7 100644 --- a/tools/poretools/test-data/poretools-tabular-out3.tabular +++ b/tools/poretools/test-data/poretools-tabular-out3.tabular @@ -1,13 +1,5 @@ length name sequence quals 202 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 GAAATTGCTGGTTGCTCCCCGAGGGGCCTATAAACAATCGGATAAGGGTCTAAGTCAGGGCGAAAAAGATTTGGGGGCTCCTAATCTCCGATAATGAGTGCCGCAACATACGGATAGTACCTTTATGCGTAACCGCTCCATACGACAAATAATTATTTATATACGGTACCTACGGAACCAAAATTGACAAGTTCGTACTTTT )))))+*,,*,*--,-,..---./0..++++-/-//**)*)))*,,.///---**)))*))+/,//-.,00.--)***+*+))),)*)))+).*----.--**..,-,**,**,+++++,+*+*)**+,,,**((+,,+,))()**+,++,+**+--,)(((((()(((((()(())))+,//),+--.+(())(((()((( -159 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 ATCGACCATATTGGCTTTTTGGTTATCCTGGTCTACCTCTTGTTGTCTTGGTGGGTGCCAACAGCTATGCATCTGTTGCATCAATCGTGACGGGAAACGAGAGGACAATTTCCCGGGTTAAACATGCCGATTGTCAGCCGCGGGGGCTGGGGAGGTTCC ""$"#$$&%$(&$"#$,<0-+(-'%(#$%$&(&%$$$%'-,(0'$)%(&$"'"#"'"$#$"&#&$##&%$%'%&'00,&'%#$##$$&"####%$'#%(''$$"$"($/=,)''#$$'%%'$'$)$%&$%()''%%"%&%%%(*#(%"$&&(&##&)&$ -212 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 CTTCTGTTGTGGTGCTCTTGCTCCCCAGGGGCCTATAAACGTGCACATAGGGTCTAAGTCAGCGAAAAAGATTTGAGGCTCCCGTATAGATAATGGATCCCCTCAGCCCTAGCTGACCGTCATCCGTAACGCCTCCATACATAAATAATTATTTAGCTCTAGTACACCCAGGCGGATCGCTTCTGGTTTTATATTTCTTGATTACTGATGCA "#')-,;42;7<8544/22.**)-(*()*(')%%&''-*0..+)%%$"'%'*/'%%&$&$%&##$%%(%)%/4)&#&'#$#$#$*#$"#&$$#'&$#*$%&##(&"*%)%&$&&&**(&(%%(%%),-%&%')*/,,(((%$%'$##","#,2''#$$('('*()(+)''&*)%$'(%#&%4.01-17;2&&$'12'')"%)&#$#"$)&'# 413 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 GCTTCTTCTGCTTATATTGCTTAGAAGGAAATACGAGAGGAGAAAGAGTAGATGATGATAAAGGGTCGACTAATTATTTCCGAAGTTTGTTAAAGTCGAAATCGCTTCGAATTTGAAATTGTTGCTGACGCAAGTTAGCGATGCGCGATCCCAGGAGTATAGGGGTTGAAAACGGTTCCATTTGATAAGGTTTTCCATTAATGACGTCACGTTGTTTGGTATTTCCTTCTATTTTCTCCGAAGCGCCCCTCTCTCTCTCATCTCACGTCAGATTCAATTTTATTACAACAAATGTGAAAAGTGGGTTCGCAGAGGTCGCTTAAGCCATTTTCTTAGATACAGCTTGAAAACGAATCTACAGAACAAATCTCCTGCCATTACACTCAGAGTCATGACGGTCGTGTTTATAGAGT ))****-+.,,,++,,-,...-*++/,0.1,++,,..-0/)+-/,----,+,,,-,--,-+****+**+**+-.-.0500-.0-,,+*,.,,,,+-*+./.++,.////10+/,/03/10/.0..-*--./0001.--.++../////0--,./0//****.//..--).0-,-*,,+*)10,+-+++,,./+,+++*)+-++++**)))*))*)+*+,*,.0,.+,****,--)))*)()+(*))))))))**,,,,*))((*))**))(*++(+*-,-,())))**+-0-*****./,)****-0/..,-,,.--,-+,****-./680/--*)+000/.//-,/03/..0--.*,++*+*)**)*)*++++.//0/,++**+))*+++*)))**++-,-,3520...**) -376 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 ACTCTAACTCAGGCTGGTATCTGAGTGTAATGGCGCAGTTGTCTGTAGGGTCGTTCAAGCTGTATCAAGAAATGAGTAAGCGAAAACCTGCGAGCCGATTTTCGCTTTGTTTAGTAAGGTTAGTGACGTGAGGGTGAGAGAGAGAGAGAGCGTTCGGAGAAAATAGAAGGAGAACCCAAACAACGTGACGTCATTGATGAAAACCTTATCGGGAACCCGTTTCAACCCCTATACTCCTCGGCGCGTAGGCTAACTGCGTAGCAACATTCAATTCAGCAGTTTTCCTGTCAGCGACTTCGGAAGCTTAGTCAACAGTGTTTATCAGCTCCTCTTCCTCTCGTATTTCGTTCAAGCAATATAGCAGAGGCGCCTGTCC "$###$$$#%#$"###$'###$"&'.)*(*+,-)$%$&/&$1(*),&&%%('$1)%##%%))+((%#$+&*%&&%$%%'(*,--+()$+-+),#*'%')4:*'$$*:,')'#%#%$&%$+++$*%$'&&)&&&&')'+*-,+*'&*$)%'&&'')'*)+,--'&&'$)(2&$)%%&(&&$&%#%%)$%&&((*(+$')(&(%##'+,+,)'((%%$%(*02*')&))+'"%$%%&'$#&%$$(#$&$%%##'&&,*))*((&%#(%*,(*(**$'()%#*=?/-&*)*(##&%'&+,(+*,)%'&*+*+('%($#'#*2+('%$$$&&%#$(+(('''(')'+30,$)*'((*('&&%#$$%%&%''$'$%&&1/$ -373 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 CATTCTTTGGTGCTGATCCTGCGAGGAGAGGGGGAGGGGAACAATGGTAGCCACTAAATCTATAACAATTATTTCAGAAGTTGTCCGCTTGAATCATTCATTTGAAATTGTTAGTGACGCAAGTTAATGCGCGATCCCAGGAGCGGGCTCGTCCAGTTTACAATTGTCCATGCGTAGTCAGTTGTTATGTTGATTCCTGTTACCGATAGGGTATATAACGCTCCTAGTCGATTCGATTTGCTTGGCGCCATCCAAGTATTCCAGAGTCCTTAGCATTTTCTTAATGGCACGTGAAAACGAATCCCCTAAGAGCCACTTATCACGTCCGATTACATACTCCAGTCATGACGCTTCTGTTTATGTTTCTTAACCA ##''$%)0%%)$&''',&'(&&$-+*-'('*+(('$$&#'#$%$%##$$#%$$#"$%$'$##$%"%#%)&$,5+($),,*0(&,####&)()(**)+)&$&,$&%1,3-*.''#'#$'('/*)+&&&+$&'%()*((%%)$&$#####"$%3%)')5/($$##&*$0%&()#$%%$$&'%(+%&-)%&%,-##((%$%&)*%&&#%""####"#"$$##""#('#$''$$&)0(&(.//$$&&###%&&+%('&%##%+)&&'%$#&%#%$#"(%/FA/+,(&'##$&%%#(&%*1)*()'())*("#$$(%%(&%*%$$$"$#($%##+$$%$####%$'&((&&$$%$)'1.+*:7,))',7&%)#$#$$# 523 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 ATGTTTCTTCAGTGATACCTGTGACATCCGGAAAGGAGGAGGAGGATCAGAAAGGAGGAGTGTGACATAACGCTGACAGTGCGTGCTTAGGTTCGTTAATAAACAAAGCCATATTACGGAGATGGCGTAATCACCTACGATGAAAGTGGTCACGTACGCGTGCCACCTGGGCATCGTCCTCACCCCTTCATTAAATTACAGGCTTTTGACTCCTTCAACCTTCTCGTTGTAATTGGTTAGTACTTATCCTATCTTATTCGCGATCGGCGTTCGATTGGATTTCGCTTCGAATGTAATCCGTATGCGCAATACAAATATTTGAGCTAATTTCCTCTCTTTACGTAATCGTTTTCGTCACCGTCGTCAATTATCGATACGGGAATCAAGTCGAACGAACCCCTGACCGAGAATCAGAAAAACTTTCAGAAGAAAAAGGAAGAAGAGAAAGCTCTTTCACATTGTAAACCAAACGCGAAAGCTCCCGAAAACAAAGGGCGGCGATTCTAAACATTTGGTTTATGTT (((*-,+,,,++*()(())*-)),....+/-,.),-++--./-,))*()))+*+*)*-*,**)())((*)(*()(*--+**)()()*(())))*,--*,+,.,---+)+))()**((())*+,-/./,--,++****+,+,,-02.///..-.--...,,))))))*++,+*++,+++*)*++-+*+**)+++**+)))(((())+*()((()(()))))))((((),-./--+*)))((((()((((((*+,,+,*+*,++++****,1.+*++,+,-.2-,+,-,+*,*.-.1/----*+,*+**++***./.-+*-+))))*,,-/*-*****-,*))))**,+++-,++++*+*,-../.-,**)*)+******-+,+)*++*+-.//../..,,+,..+.)+-+,))*+*++,+*,----.//-0662.-,--.-0.../.,+))-,2/.-++*****+**++++-+-...+,+*****,,.,+*.+,,,++*)))+/.,-10,+***)**++***+* -464 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 GAACACAACTGTTTCCCAGTACACGCTTTGTTTAAGCTTTCGCGTTGGTTCCATGTGAAGAGCTTCTGTTCTTCCTTTTTTGGTATGAAAGTTTTAGTTCTCTTCAGAGTCGTCCCACTTGATGTCCCGTATCGCTTGTGGACATTGTAGAAATGATCGTAAGGGCAGAGGAATTAATTAAAACTTTGTGGTGCCATCCCATTACGGTCGAGCGAATCCAGTAGCACCAGTACCCAGTAAGAACGAACCCTGAGCCAATTACACAGAAGGTTGAAGGAGTCAAGCTGTAGTTGGAAGGGGTGAAGGTCCGCACAAGATTCGATCCTCGTTATCGTACCTGATTACACATCTCTGCGTGATATGATGATTCTTTATTAGCAACCGAGCACGCACTGTTGGCGTTATGTTCGGATACTACGGTCTATCCTCTCAAACGGTCCAGCTCCCAACATCGGCGTCAGTCA #"#$"$%%#$#*3.$%&%$(#$%#$#'-,(4*$#$$%(2+'&%%*.%%,:'%&,)*,'%(%%$*,'''(*(%,'%)2>B>/'#$$&&$)+%/;,&#$()'&'&&($%#$(&&*&$$$#%%$$'&)+%&$)#%$##%'%&%#$$#&-%##&$&$#$#%$$$%&##&$$$&,-('(###'$')'#$+14(&$$($%$%#$&#'*+)*%)+$$&%$'&&(%&&%)"%$$'&%#)#%'#'$'%'(%&%%&%&%#$###&#&'+&####$($$$#'*)(+,-*$)&&'$&%$$$$((%+'&&$%#''$$$#&$%%$#$$$,%(*&"#&###(&*$%%%$&#$$%$&)+()$(&'$%$$##$)"&$#$##$&#&.#&1)&(%%'%&#'%#&&&%$&%$%(',('('&)+&%%-&#"$#%$%$$'$$,)(),'%%$$$###'##*((%(%%'%#$##"%##$(*-)&'&%# -494 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 TTGTGTTTCTTCTTATGACTTGCTATGCGCAGGGGGGAGGAGAGATGTAGCGGAGGGCAGAGTGTGAAAGGGGTAGTTCATTATGCTGTCGTTAAGCCTCCGGGGCTATTGAAAACGATGAATGGGGCCAGGCGCTGGTCACGTACACGTGCGACACTGATGAAACGTTCCTCACCATTCATTAAATTACCGGCTTTTAAACGTGAACATGCTGTTGTAATTCTTCATGGTGGTGTAATGTACTTAGCAGTAGCGTTCAATTGGATTTCGCTTCGAATGTAGTCGATCTGCGCATCCACTGGTCGACGATTTCCTCTCTTTACTGATCGTAGTTCGTCACGTCGTCGTACGATAGGATCAAAGTCGCGGGATGGCTATCCCCGGGCGAACTTTCCAGAGAAGGAAGAAGAAAGACCTTTCGGCTTGTAGTAAGACCCCGAAGACTCGAAAACAGGGCAACGCGAATTCCACTTCGTTATGTTCTTACTATTGGA #$$*)*8+$()&(%%$#$#&'$#"%%#$($+&,&(-(',.,*%$%%$$$"$$('%%'&('%%%%%$##$#$$"$#$%&%$&$#'$$#$)''+&$%"&##($#$$###$*&*$&(%%$&($&$&"###%$$#&"#!%$$($$%$'$&%&'*%&$#$#$%$$$($/$/.2)'$#%#%(#**)%)&'$#)%#%''(%')0'$%#$$'$&#$#&$&$&,2-,/%1,"%*%%$#%&##%%&)((('&%(&&%'*%&'$((-:'%(**)((/5)%$&,,*%)#'%$$#&$"#'$)$&%%%#$$%#$#"'$"#$"$17)&##%&')3'##$$$$$#%#%+)'&)&#+*,)&'%%&#%#%#$*%&%$%%##&&#%%'#'#$$%##$%)$'%%'%#'$#)48$$#%#'#*)-,,))')((%#$#&&-'(##'%*%$&"""$#$#')%$'($$#"'$&&)$&'%(*&%%'$$)+)6*(#%#%'%&*,)(&3*$%'$%%$(,,&# 692 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 CATGTTTCTGCTGATATTGCTAATGGCTGAACTGGAAATAAGGATCCGTTGCTTGCCAACAACTATACTGCGTGGTATTTTCCCAGTGGAAAGATCGGGAACCTTTGATCTTCAATATAGTTACAATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTTGGGTATAACAGGATGAGGAGGACGATTCGAAGTCACGATCATGCGCCCAAGTCAGAATGACTCCACACTACTCCTCCTCAGGACCATTTATAAATAAACAGTGATCAAGATTCCAACAATTAAGATGGCTTGAAACCAATTTCTGCTCTTGTTTTTGTTCCCACTCCCCCCTCCCCCCGAGGTCAGGATGAAGTATTAACTCTGAAGATAAAGGACCCCACGACGACAACGGCTTCCAGTTACTTCGAAGGCATTTTTCTACTTCTACTTCCCCTCCGTCTCATCCTCCTCCTCAGCTACCAAATTCACAATAGGACCGCAGGAAAAGTCTGTAGCGAATAGAACCTTCTTCACTACGGTTTCGTACCTAAAATGTTCTGGAAAAATGGATAGAAAAGAATCTTTTAAAATCGAAATCCGATTTTCGGAGTGTTAACAATGTAACTGTTGTAGAAAAGGAGCGGTAAATGAGACGTGGGGAATAAGATACAGAGCAACCACTGTCGTTAAGGACCGTTTGAGTGTTT ))))+-*)*)+**++**+)*)*,-,,+++-+++/./20.//.+...*.,-,--+***,+++++**+++,.//.,++,.54.320/--.,-.++-.,,.-++++*,+,-./0/.0000/..0-,----/.----,+++++,00.//./.++*+//0.//00/285/+*+**+-,,,,,-,**,,,+--00*0/)*.,+,+.,,,+++,,-+*,*+-+,+,--..,+****)**+++,+++***)*+)**)-,.20//02-))**++*+**+*+**-/0./-,,,--))*))++)+*++..,,+-./.+++++,++++,025-,5.-/,-//0/---,,.43430,,-+,+,.,/..-.+***)))))..//-+,***)))+)++))),***)**))(())--.-())((,((*(*(((*+-0/---,*/**)*,-/.0.-,.,++)*,+,,-,--,-,+++**))**,+*+*))))*))))*))+(+,-+,**)))*)*)))*++((*+****,,,---+*,+*+,0,++*)))(,03.--1+***-*-)*)+****))))+))+***+21--/.-)))**)*)***-10--,-,,+*+)))+,..,,/,,,,-,+)())***)())*++++,+)))***+*))((,+(((())(*)()()***,,---,,,+)((((,()**.*(***+))) -602 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 ACACTAGCATCTGTCTGGCCCCGATATTTGTAGTATGTACTTTACGTGTACTGTTACTATGGTATTTTCACCCTCAGTTTGCCCTTGTCACTCGAAAGTCGAATTCAGTGTTTTAAAAGATTGTCTGGTTCTATCGGTTCCGAGCAGTTTTAATAGAACTGATCAATGAAGAAGGTTCGTTCGAGCGAACTTCCAGTGATCTTGTGAATTTGAGCTGAGGAGGAGATGAAAGAGGGAAGTAGAAGTAGAAAAATTGCATCGAAATATGGAATAAATTGTATCGTCGGTCTTGCTTTTATCTGTCAGTTATACTTCAGTAGGAGGGAGTGGGATAACGACAGCAATTAGTTCAGCCTTAGTGTTGAGGAATCTGGTTCTTTAACATCTTTGGTGGGAGGAGTGTCCTTGATTTAATATGCAGAAGTATCCTTGCTGCGAATCGTCATCATCCTTTAACAATAGGATGAAAACCGTTAAAATGCCGACAGTTGGACCTGCGAGCCGCCGGCCCGTATTCATGGGAAAGTACCGCATTAACGTGTGTCAGGCGGGACGTATTATTTCCCGTTCAGCCGATTAAGTATACAGGCACAGAGACTTCC ####"##&%##$#+%%##%#'%#$%$)-)'($%&&((,()+-'&'(($%#(&%1-$##$'$#%#'08+'$$%#"&$#&.+$%*#('%%##$$&&)))$(''($(('##+)6<4)'(*()',,(.'&%&'*($%&%##-,('#$$"$$'04)&%$#('&%%%%'$##(%%$*$'$#'''&),%$%$%$%$$$*+%$%(%%&&''%%(&%1-(%$"#%&&+**-,'&''((&#'#$&%'&%'#(&+#)*))//+&&%$%$%$%&)&&$),-*&%$$$&)%$#$'&+(#%'&''$##(2(%&$%$..('($&%%*.+'$%%%),')'()%*'&)%#&##"###&%%%'*$'++($$%#'%%"($)&#$%''&(**)$+*&)3-&%$$$#$)&$%'%)*')&&$%%&$#&($#+0&$"##%###'%(%'&(%$%(%#&$%$&$&$#%###$$&$%&+&&$$%&$$'('&(&&&#%$$'%%&'%'"%###$$#-)%#$#%'%%$&'''"&%$$'%$$)#(-*&)+09))'#'#%&%&$$(&%%%)(+()&%$('"""$"#&#'$$'./(*&&('%$#$$##'%$&$&%$"&"))##$#'$##"$)'$ -657 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 GTATTTCTTATGATATTAGATGTAGGCTGGAAATAGAATGCGTGCTTTACAGGCCTCCTCTGCGTATGTTTCCATGGAAGCCGTAGGAACCTTTGATCTTCATACTTGCCCTATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTGATATAACAGGATACGGAAAGAGTTCGAAGTCGAATCGTCCAGCAAGTCGAATGACTCTAAAGACATCGGCACGGCCTTTGAGGCTCGTATATGCCTAATTCCAACAATGCAAAGTACGTGGAACAGATTTCTGCTCTTTTTTGTTCCACTCCGCCAGCCCCCCGAGGTCAGGATGAAATATTACTCTGAAAACCGCCAACCCACGGGACAGCTACGTCGAATGTCGTCGAACAGTTCTATTCCTTCCCCTCCGTTAGTACTACTCTAGGCTACTCAATTCAGGCGATAGAAGGAAAAGTCTGTACCAGGCGGGTTCTTCGGCTTTTCAATGCGCGCTGTTCTGGGGAGCTATCGCTGCAAAGAATCTTTTAAAATCGAGTCGAGTTTTCAGAGTGTTCCTCAATGTAACTGTTGGCAAAGGAGCGGGCCTGGCAGACGTGGGGAATAAGACCCCAAAACCACTTCGTGCACATCGTTCTGGTGTTCATCTGTTCTTAGCTCTTGT "##)7.'-(&&$$&#'$$$''%$%$&(),210)&&)&)+&.-+'((,%#))())&%)(')+)*+.***CC/&'$'')(*###$&%)5)1')&./%%)%++)&%$%%.#''(#%*)+&&).*)'*%$+A/'&%+%)''-;+)-'++-1)9>0()((%&%&&(')%$%#+-/&'#%+3&**/&''&'%'%$($%&$'(&'(&)*++)('&'#$$#"#"#%'$&%#$#")$&.'#&$%$$$$($&#)#%$#%,10*)%$&$,)&'"%#"%$&%1&')&%%%'-A:10/,+(*0KLI,,I330,**.,$&$'&,7255.)+(%'&&+$,%%%'$$$&&%$$&''$*)$$%#%$&$'%#$$$#"##$$%$$(#*'#$&%#&$#$$$(%&%'1)'%$/,(')3+0-,,1*)0$##'#$%$&&(#$$##"#$#'&$,(&&#$%$&$$)&+,++**(%+'&&%$$$%"$"#%$,5')(''&',:M/($&,&($%$$((7,&%%--$&$##$%$$%))$+*',.--+-3/'$')%&##&$*($''-3E3)$)'&('&)#&&())+)))('(&/*))',-&0**('&%#$##$)#'&+,,(&&&%)'%%$%&&*+&%$%"#$$$%)(()%&"#&#)&1.+,**++-C$&$$&$4(%)$$##$#$&$% diff --git a/tools/poretools/test-data/poretools-tabular-out4.tabular b/tools/poretools/test-data/poretools-tabular-out4.tabular index 2690807f14b..ce9fa1cfcb7 100644 --- a/tools/poretools/test-data/poretools-tabular-out4.tabular +++ b/tools/poretools/test-data/poretools-tabular-out4.tabular @@ -1,13 +1,5 @@ length name sequence quals 202 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 GAAATTGCTGGTTGCTCCCCGAGGGGCCTATAAACAATCGGATAAGGGTCTAAGTCAGGGCGAAAAAGATTTGGGGGCTCCTAATCTCCGATAATGAGTGCCGCAACATACGGATAGTACCTTTATGCGTAACCGCTCCATACGACAAATAATTATTTATATACGGTACCTACGGAACCAAAATTGACAAGTTCGTACTTTT )))))+*,,*,*--,-,..---./0..++++-/-//**)*)))*,,.///---**)))*))+/,//-.,00.--)***+*+))),)*)))+).*----.--**..,-,**,**,+++++,+*+*)**+,,,**((+,,+,))()**+,++,+**+--,)(((((()(((((()(())))+,//),+--.+(())(((()((( -159 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 ATCGACCATATTGGCTTTTTGGTTATCCTGGTCTACCTCTTGTTGTCTTGGTGGGTGCCAACAGCTATGCATCTGTTGCATCAATCGTGACGGGAAACGAGAGGACAATTTCCCGGGTTAAACATGCCGATTGTCAGCCGCGGGGGCTGGGGAGGTTCC ""$"#$$&%$(&$"#$,<0-+(-'%(#$%$&(&%$$$%'-,(0'$)%(&$"'"#"'"$#$"&#&$##&%$%'%&'00,&'%#$##$$&"####%$'#%(''$$"$"($/=,)''#$$'%%'$'$)$%&$%()''%%"%&%%%(*#(%"$&&(&##&)&$ -212 @b7b29e94-0894-415c-87c4-a809bc8e8bdb_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read95_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 CTTCTGTTGTGGTGCTCTTGCTCCCCAGGGGCCTATAAACGTGCACATAGGGTCTAAGTCAGCGAAAAAGATTTGAGGCTCCCGTATAGATAATGGATCCCCTCAGCCCTAGCTGACCGTCATCCGTAACGCCTCCATACATAAATAATTATTTAGCTCTAGTACACCCAGGCGGATCGCTTCTGGTTTTATATTTCTTGATTACTGATGCA "#')-,;42;7<8544/22.**)-(*()*(')%%&''-*0..+)%%$"'%'*/'%%&$&$%&##$%%(%)%/4)&#&'#$#$#$*#$"#&$$#'&$#*$%&##(&"*%)%&$&&&**(&(%%(%%),-%&%')*/,,(((%$%'$##","#,2''#$$('('*()(+)''&*)%$'(%#&%4.01-17;2&&$'12'')"%)&#$#"$)&'# 413 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 GCTTCTTCTGCTTATATTGCTTAGAAGGAAATACGAGAGGAGAAAGAGTAGATGATGATAAAGGGTCGACTAATTATTTCCGAAGTTTGTTAAAGTCGAAATCGCTTCGAATTTGAAATTGTTGCTGACGCAAGTTAGCGATGCGCGATCCCAGGAGTATAGGGGTTGAAAACGGTTCCATTTGATAAGGTTTTCCATTAATGACGTCACGTTGTTTGGTATTTCCTTCTATTTTCTCCGAAGCGCCCCTCTCTCTCTCATCTCACGTCAGATTCAATTTTATTACAACAAATGTGAAAAGTGGGTTCGCAGAGGTCGCTTAAGCCATTTTCTTAGATACAGCTTGAAAACGAATCTACAGAACAAATCTCCTGCCATTACACTCAGAGTCATGACGGTCGTGTTTATAGAGT ))****-+.,,,++,,-,...-*++/,0.1,++,,..-0/)+-/,----,+,,,-,--,-+****+**+**+-.-.0500-.0-,,+*,.,,,,+-*+./.++,.////10+/,/03/10/.0..-*--./0001.--.++../////0--,./0//****.//..--).0-,-*,,+*)10,+-+++,,./+,+++*)+-++++**)))*))*)+*+,*,.0,.+,****,--)))*)()+(*))))))))**,,,,*))((*))**))(*++(+*-,-,())))**+-0-*****./,)****-0/..,-,,.--,-+,****-./680/--*)+000/.//-,/03/..0--.*,++*+*)**)*)*++++.//0/,++**+))*+++*)))**++-,-,3520...**) -376 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 ACTCTAACTCAGGCTGGTATCTGAGTGTAATGGCGCAGTTGTCTGTAGGGTCGTTCAAGCTGTATCAAGAAATGAGTAAGCGAAAACCTGCGAGCCGATTTTCGCTTTGTTTAGTAAGGTTAGTGACGTGAGGGTGAGAGAGAGAGAGAGCGTTCGGAGAAAATAGAAGGAGAACCCAAACAACGTGACGTCATTGATGAAAACCTTATCGGGAACCCGTTTCAACCCCTATACTCCTCGGCGCGTAGGCTAACTGCGTAGCAACATTCAATTCAGCAGTTTTCCTGTCAGCGACTTCGGAAGCTTAGTCAACAGTGTTTATCAGCTCCTCTTCCTCTCGTATTTCGTTCAAGCAATATAGCAGAGGCGCCTGTCC "$###$$$#%#$"###$'###$"&'.)*(*+,-)$%$&/&$1(*),&&%%('$1)%##%%))+((%#$+&*%&&%$%%'(*,--+()$+-+),#*'%')4:*'$$*:,')'#%#%$&%$+++$*%$'&&)&&&&')'+*-,+*'&*$)%'&&'')'*)+,--'&&'$)(2&$)%%&(&&$&%#%%)$%&&((*(+$')(&(%##'+,+,)'((%%$%(*02*')&))+'"%$%%&'$#&%$$(#$&$%%##'&&,*))*((&%#(%*,(*(**$'()%#*=?/-&*)*(##&%'&+,(+*,)%'&*+*+('%($#'#*2+('%$$$&&%#$(+(('''(')'+30,$)*'((*('&&%#$$%%&%''$'$%&&1/$ -373 @935c5941-a78e-4959-923e-f71157063e92_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch128_read430_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 CATTCTTTGGTGCTGATCCTGCGAGGAGAGGGGGAGGGGAACAATGGTAGCCACTAAATCTATAACAATTATTTCAGAAGTTGTCCGCTTGAATCATTCATTTGAAATTGTTAGTGACGCAAGTTAATGCGCGATCCCAGGAGCGGGCTCGTCCAGTTTACAATTGTCCATGCGTAGTCAGTTGTTATGTTGATTCCTGTTACCGATAGGGTATATAACGCTCCTAGTCGATTCGATTTGCTTGGCGCCATCCAAGTATTCCAGAGTCCTTAGCATTTTCTTAATGGCACGTGAAAACGAATCCCCTAAGAGCCACTTATCACGTCCGATTACATACTCCAGTCATGACGCTTCTGTTTATGTTTCTTAACCA ##''$%)0%%)$&''',&'(&&$-+*-'('*+(('$$&#'#$%$%##$$#%$$#"$%$'$##$%"%#%)&$,5+($),,*0(&,####&)()(**)+)&$&,$&%1,3-*.''#'#$'('/*)+&&&+$&'%()*((%%)$&$#####"$%3%)')5/($$##&*$0%&()#$%%$$&'%(+%&-)%&%,-##((%$%&)*%&&#%""####"#"$$##""#('#$''$$&)0(&(.//$$&&###%&&+%('&%##%+)&&'%$#&%#%$#"(%/FA/+,(&'##$&%%#(&%*1)*()'())*("#$$(%%(&%*%$$$"$#($%##+$$%$####%$'&((&&$$%$)'1.+*:7,))',7&%)#$#$$# 523 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 ATGTTTCTTCAGTGATACCTGTGACATCCGGAAAGGAGGAGGAGGATCAGAAAGGAGGAGTGTGACATAACGCTGACAGTGCGTGCTTAGGTTCGTTAATAAACAAAGCCATATTACGGAGATGGCGTAATCACCTACGATGAAAGTGGTCACGTACGCGTGCCACCTGGGCATCGTCCTCACCCCTTCATTAAATTACAGGCTTTTGACTCCTTCAACCTTCTCGTTGTAATTGGTTAGTACTTATCCTATCTTATTCGCGATCGGCGTTCGATTGGATTTCGCTTCGAATGTAATCCGTATGCGCAATACAAATATTTGAGCTAATTTCCTCTCTTTACGTAATCGTTTTCGTCACCGTCGTCAATTATCGATACGGGAATCAAGTCGAACGAACCCCTGACCGAGAATCAGAAAAACTTTCAGAAGAAAAAGGAAGAAGAGAAAGCTCTTTCACATTGTAAACCAAACGCGAAAGCTCCCGAAAACAAAGGGCGGCGATTCTAAACATTTGGTTTATGTT (((*-,+,,,++*()(())*-)),....+/-,.),-++--./-,))*()))+*+*)*-*,**)())((*)(*()(*--+**)()()*(())))*,--*,+,.,---+)+))()**((())*+,-/./,--,++****+,+,,-02.///..-.--...,,))))))*++,+*++,+++*)*++-+*+**)+++**+)))(((())+*()((()(()))))))((((),-./--+*)))((((()((((((*+,,+,*+*,++++****,1.+*++,+,-.2-,+,-,+*,*.-.1/----*+,*+**++***./.-+*-+))))*,,-/*-*****-,*))))**,+++-,++++*+*,-../.-,**)*)+******-+,+)*++*+-.//../..,,+,..+.)+-+,))*+*++,+*,----.//-0662.-,--.-0.../.,+))-,2/.-++*****+**++++-+-...+,+*****,,.,+*.+,,,++*)))+/.,-10,+***)**++***+* -464 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 GAACACAACTGTTTCCCAGTACACGCTTTGTTTAAGCTTTCGCGTTGGTTCCATGTGAAGAGCTTCTGTTCTTCCTTTTTTGGTATGAAAGTTTTAGTTCTCTTCAGAGTCGTCCCACTTGATGTCCCGTATCGCTTGTGGACATTGTAGAAATGATCGTAAGGGCAGAGGAATTAATTAAAACTTTGTGGTGCCATCCCATTACGGTCGAGCGAATCCAGTAGCACCAGTACCCAGTAAGAACGAACCCTGAGCCAATTACACAGAAGGTTGAAGGAGTCAAGCTGTAGTTGGAAGGGGTGAAGGTCCGCACAAGATTCGATCCTCGTTATCGTACCTGATTACACATCTCTGCGTGATATGATGATTCTTTATTAGCAACCGAGCACGCACTGTTGGCGTTATGTTCGGATACTACGGTCTATCCTCTCAAACGGTCCAGCTCCCAACATCGGCGTCAGTCA #"#$"$%%#$#*3.$%&%$(#$%#$#'-,(4*$#$$%(2+'&%%*.%%,:'%&,)*,'%(%%$*,'''(*(%,'%)2>B>/'#$$&&$)+%/;,&#$()'&'&&($%#$(&&*&$$$#%%$$'&)+%&$)#%$##%'%&%#$$#&-%##&$&$#$#%$$$%&##&$$$&,-('(###'$')'#$+14(&$$($%$%#$&#'*+)*%)+$$&%$'&&(%&&%)"%$$'&%#)#%'#'$'%'(%&%%&%&%#$###&#&'+&####$($$$#'*)(+,-*$)&&'$&%$$$$((%+'&&$%#''$$$#&$%%$#$$$,%(*&"#&###(&*$%%%$&#$$%$&)+()$(&'$%$$##$)"&$#$##$&#&.#&1)&(%%'%&#'%#&&&%$&%$%(',('('&)+&%%-&#"$#%$%$$'$$,)(),'%%$$$###'##*((%(%%'%#$##"%##$(*-)&'&%# -494 @e643ceef-570f-4ba7-bdae-e9e78da71703_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read1377_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 TTGTGTTTCTTCTTATGACTTGCTATGCGCAGGGGGGAGGAGAGATGTAGCGGAGGGCAGAGTGTGAAAGGGGTAGTTCATTATGCTGTCGTTAAGCCTCCGGGGCTATTGAAAACGATGAATGGGGCCAGGCGCTGGTCACGTACACGTGCGACACTGATGAAACGTTCCTCACCATTCATTAAATTACCGGCTTTTAAACGTGAACATGCTGTTGTAATTCTTCATGGTGGTGTAATGTACTTAGCAGTAGCGTTCAATTGGATTTCGCTTCGAATGTAGTCGATCTGCGCATCCACTGGTCGACGATTTCCTCTCTTTACTGATCGTAGTTCGTCACGTCGTCGTACGATAGGATCAAAGTCGCGGGATGGCTATCCCCGGGCGAACTTTCCAGAGAAGGAAGAAGAAAGACCTTTCGGCTTGTAGTAAGACCCCGAAGACTCGAAAACAGGGCAACGCGAATTCCACTTCGTTATGTTCTTACTATTGGA #$$*)*8+$()&(%%$#$#&'$#"%%#$($+&,&(-(',.,*%$%%$$$"$$('%%'&('%%%%%$##$#$$"$#$%&%$&$#'$$#$)''+&$%"&##($#$$###$*&*$&(%%$&($&$&"###%$$#&"#!%$$($$%$'$&%&'*%&$#$#$%$$$($/$/.2)'$#%#%(#**)%)&'$#)%#%''(%')0'$%#$$'$&#$#&$&$&,2-,/%1,"%*%%$#%&##%%&)((('&%(&&%'*%&'$((-:'%(**)((/5)%$&,,*%)#'%$$#&$"#'$)$&%%%#$$%#$#"'$"#$"$17)&##%&')3'##$$$$$#%#%+)'&)&#+*,)&'%%&#%#%#$*%&%$%%##&&#%%'#'#$$%##$%)$'%%'%#'$#)48$$#%#'#*)-,,))')((%#$#&&-'(##'%*%$&"""$#$#')%$'($$#"'$&&)$&'%(*&%%'$$)+)6*(#%#%'%&*,)(&3*$%'$%%$(,,&# 692 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 CATGTTTCTGCTGATATTGCTAATGGCTGAACTGGAAATAAGGATCCGTTGCTTGCCAACAACTATACTGCGTGGTATTTTCCCAGTGGAAAGATCGGGAACCTTTGATCTTCAATATAGTTACAATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTTGGGTATAACAGGATGAGGAGGACGATTCGAAGTCACGATCATGCGCCCAAGTCAGAATGACTCCACACTACTCCTCCTCAGGACCATTTATAAATAAACAGTGATCAAGATTCCAACAATTAAGATGGCTTGAAACCAATTTCTGCTCTTGTTTTTGTTCCCACTCCCCCCTCCCCCCGAGGTCAGGATGAAGTATTAACTCTGAAGATAAAGGACCCCACGACGACAACGGCTTCCAGTTACTTCGAAGGCATTTTTCTACTTCTACTTCCCCTCCGTCTCATCCTCCTCCTCAGCTACCAAATTCACAATAGGACCGCAGGAAAAGTCTGTAGCGAATAGAACCTTCTTCACTACGGTTTCGTACCTAAAATGTTCTGGAAAAATGGATAGAAAAGAATCTTTTAAAATCGAAATCCGATTTTCGGAGTGTTAACAATGTAACTGTTGTAGAAAAGGAGCGGTAAATGAGACGTGGGGAATAAGATACAGAGCAACCACTGTCGTTAAGGACCGTTTGAGTGTTT ))))+-*)*)+**++**+)*)*,-,,+++-+++/./20.//.+...*.,-,--+***,+++++**+++,.//.,++,.54.320/--.,-.++-.,,.-++++*,+,-./0/.0000/..0-,----/.----,+++++,00.//./.++*+//0.//00/285/+*+**+-,,,,,-,**,,,+--00*0/)*.,+,+.,,,+++,,-+*,*+-+,+,--..,+****)**+++,+++***)*+)**)-,.20//02-))**++*+**+*+**-/0./-,,,--))*))++)+*++..,,+-./.+++++,++++,025-,5.-/,-//0/---,,.43430,,-+,+,.,/..-.+***)))))..//-+,***)))+)++))),***)**))(())--.-())((,((*(*(((*+-0/---,*/**)*,-/.0.-,.,++)*,+,,-,--,-,+++**))**,+*+*))))*))))*))+(+,-+,**)))*)*)))*++((*+****,,,---+*,+*+,0,++*)))(,03.--1+***-*-)*)+****))))+))+***+21--/.-)))**)*)***-10--,-,,+*+)))+,..,,/,,,,-,+)())***)())*++++,+)))***+*))((,+(((())(*)()()***,,---,,,+)((((,()**.*(***+))) -602 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 ACACTAGCATCTGTCTGGCCCCGATATTTGTAGTATGTACTTTACGTGTACTGTTACTATGGTATTTTCACCCTCAGTTTGCCCTTGTCACTCGAAAGTCGAATTCAGTGTTTTAAAAGATTGTCTGGTTCTATCGGTTCCGAGCAGTTTTAATAGAACTGATCAATGAAGAAGGTTCGTTCGAGCGAACTTCCAGTGATCTTGTGAATTTGAGCTGAGGAGGAGATGAAAGAGGGAAGTAGAAGTAGAAAAATTGCATCGAAATATGGAATAAATTGTATCGTCGGTCTTGCTTTTATCTGTCAGTTATACTTCAGTAGGAGGGAGTGGGATAACGACAGCAATTAGTTCAGCCTTAGTGTTGAGGAATCTGGTTCTTTAACATCTTTGGTGGGAGGAGTGTCCTTGATTTAATATGCAGAAGTATCCTTGCTGCGAATCGTCATCATCCTTTAACAATAGGATGAAAACCGTTAAAATGCCGACAGTTGGACCTGCGAGCCGCCGGCCCGTATTCATGGGAAAGTACCGCATTAACGTGTGTCAGGCGGGACGTATTATTTCCCGTTCAGCCGATTAAGTATACAGGCACAGAGACTTCC ####"##&%##$#+%%##%#'%#$%$)-)'($%&&((,()+-'&'(($%#(&%1-$##$'$#%#'08+'$$%#"&$#&.+$%*#('%%##$$&&)))$(''($(('##+)6<4)'(*()',,(.'&%&'*($%&%##-,('#$$"$$'04)&%$#('&%%%%'$##(%%$*$'$#'''&),%$%$%$%$$$*+%$%(%%&&''%%(&%1-(%$"#%&&+**-,'&''((&#'#$&%'&%'#(&+#)*))//+&&%$%$%$%&)&&$),-*&%$$$&)%$#$'&+(#%'&''$##(2(%&$%$..('($&%%*.+'$%%%),')'()%*'&)%#&##"###&%%%'*$'++($$%#'%%"($)&#$%''&(**)$+*&)3-&%$$$#$)&$%'%)*')&&$%%&$#&($#+0&$"##%###'%(%'&(%$%(%#&$%$&$&$#%###$$&$%&+&&$$%&$$'('&(&&&#%$$'%%&'%'"%###$$#-)%#$#%'%%$&'''"&%$$'%$$)#(-*&)+09))'#'#%&%&$$(&%%%)(+()&%$('"""$"#&#'$$'./(*&&('%$#$$##'%$&$&%$"&"))##$#'$##"$)'$ -657 @2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 GTATTTCTTATGATATTAGATGTAGGCTGGAAATAGAATGCGTGCTTTACAGGCCTCCTCTGCGTATGTTTCCATGGAAGCCGTAGGAACCTTTGATCTTCATACTTGCCCTATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTGATATAACAGGATACGGAAAGAGTTCGAAGTCGAATCGTCCAGCAAGTCGAATGACTCTAAAGACATCGGCACGGCCTTTGAGGCTCGTATATGCCTAATTCCAACAATGCAAAGTACGTGGAACAGATTTCTGCTCTTTTTTGTTCCACTCCGCCAGCCCCCCGAGGTCAGGATGAAATATTACTCTGAAAACCGCCAACCCACGGGACAGCTACGTCGAATGTCGTCGAACAGTTCTATTCCTTCCCCTCCGTTAGTACTACTCTAGGCTACTCAATTCAGGCGATAGAAGGAAAAGTCTGTACCAGGCGGGTTCTTCGGCTTTTCAATGCGCGCTGTTCTGGGGAGCTATCGCTGCAAAGAATCTTTTAAAATCGAGTCGAGTTTTCAGAGTGTTCCTCAATGTAACTGTTGGCAAAGGAGCGGGCCTGGCAGACGTGGGGAATAAGACCCCAAAACCACTTCGTGCACATCGTTCTGGTGTTCATCTGTTCTTAGCTCTTGT "##)7.'-(&&$$&#'$$$''%$%$&(),210)&&)&)+&.-+'((,%#))())&%)(')+)*+.***CC/&'$'')(*###$&%)5)1')&./%%)%++)&%$%%.#''(#%*)+&&).*)'*%$+A/'&%+%)''-;+)-'++-1)9>0()((%&%&&(')%$%#+-/&'#%+3&**/&''&'%'%$($%&$'(&'(&)*++)('&'#$$#"#"#%'$&%#$#")$&.'#&$%$$$$($&#)#%$#%,10*)%$&$,)&'"%#"%$&%1&')&%%%'-A:10/,+(*0KLI,,I330,**.,$&$'&,7255.)+(%'&&+$,%%%'$$$&&%$$&''$*)$$%#%$&$'%#$$$#"##$$%$$(#*'#$&%#&$#$$$(%&%'1)'%$/,(')3+0-,,1*)0$##'#$%$&&(#$$##"#$#'&$,(&&#$%$&$$)&+,++**(%+'&&%$$$%"$"#%$,5')(''&',:M/($&,&($%$$((7,&%%--$&$##$%$$%))$+*',.--+-3/'$')%&##&$*($''-3E3)$)'&('&)#&&())+)))('(&/*))',-&0**('&%#$##$)#'&+,,(&&&%)'%%$%&&*+&%$%"#$$$%)(()%&"#&#)&1.+,**++-C$&$$&$4(%)$$##$#$&$% diff --git a/tools/poretools/test-data/poretools-times-out2.tabular b/tools/poretools/test-data/poretools-times-out2.tabular deleted file mode 100644 index 20e6a4107a1..00000000000 --- a/tools/poretools/test-data/poretools-times-out2.tabular +++ /dev/null @@ -1,5 +0,0 @@ -channel filename read_length exp_starttime unix_timestamp duration unix_timestamp_end iso_timestamp day hour minute -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 202 1457127309 1457127626 1 1457127627 2016-03-04T21:40:26+0000 04 21 40 -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 413 1457127309 1457129549 4 1457129553 2016-03-04T22:12:29+0000 04 22 12 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 523 1457127309 1457148908 5 1457148913 2016-03-05T03:35:08+0000 05 03 35 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 692 1457127309 1457129771 6 1457129777 2016-03-04T22:16:11+0000 04 22 16 diff --git a/tools/poretools/test-data/poretools-times-out3.tabular b/tools/poretools/test-data/poretools-times-out3.tabular deleted file mode 100644 index 20e6a4107a1..00000000000 --- a/tools/poretools/test-data/poretools-times-out3.tabular +++ /dev/null @@ -1,5 +0,0 @@ -channel filename read_length exp_starttime unix_timestamp duration unix_timestamp_end iso_timestamp day hour minute -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 202 1457127309 1457127626 1 1457127627 2016-03-04T21:40:26+0000 04 21 40 -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 413 1457127309 1457129549 4 1457129553 2016-03-04T22:12:29+0000 04 22 12 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 523 1457127309 1457148908 5 1457148913 2016-03-05T03:35:08+0000 05 03 35 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 692 1457127309 1457129771 6 1457129777 2016-03-04T22:16:11+0000 04 22 16 diff --git a/tools/poretools/test-data/poretools-times-out4.tabular b/tools/poretools/test-data/poretools-times-out4.tabular deleted file mode 100644 index 20e6a4107a1..00000000000 --- a/tools/poretools/test-data/poretools-times-out4.tabular +++ /dev/null @@ -1,5 +0,0 @@ -channel filename read_length exp_starttime unix_timestamp duration unix_timestamp_end iso_timestamp day hour minute -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 202 1457127309 1457127626 1 1457127627 2016-03-04T21:40:26+0000 04 21 40 -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 413 1457127309 1457129549 4 1457129553 2016-03-04T22:12:29+0000 04 22 12 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 523 1457127309 1457148908 5 1457148913 2016-03-05T03:35:08+0000 05 03 35 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 692 1457127309 1457129771 6 1457129777 2016-03-04T22:16:11+0000 04 22 16 diff --git a/tools/poretools/test-data/poretools-times-out5.tabular b/tools/poretools/test-data/poretools-times-out5.tabular deleted file mode 100644 index 20e6a4107a1..00000000000 --- a/tools/poretools/test-data/poretools-times-out5.tabular +++ /dev/null @@ -1,5 +0,0 @@ -channel filename read_length exp_starttime unix_timestamp duration unix_timestamp_end iso_timestamp day hour minute -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read95_strand.fast5 202 1457127309 1457127626 1 1457127627 2016-03-04T21:40:26+0000 04 21 40 -128 .poretools_tmp/test-data/2016_3_4_3507_1_ch128_read430_strand.fast5 413 1457127309 1457129549 4 1457129553 2016-03-04T22:12:29+0000 04 22 12 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read1377_strand.fast5 523 1457127309 1457148908 5 1457148913 2016-03-05T03:35:08+0000 05 03 35 -126 .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 692 1457127309 1457129771 6 1457129777 2016-03-04T22:16:11+0000 04 22 16 diff --git a/tools/poretools/test-data/poretools-winner-out1.tabular b/tools/poretools/test-data/poretools-winner-out1.tabular index 0e759ce8aff..a14bf89a29c 100644 --- a/tools/poretools/test-data/poretools-winner-out1.tabular +++ b/tools/poretools/test-data/poretools-winner-out1.tabular @@ -1,2 +1,2 @@ ->2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 -CATGTTTCTGCTGATATTGCTAATGGCTGAACTGGAAATAAGGATCCGTTGCTTGCCAACAACTATACTGCGTGGTATTTTCCCAGTGGAAAGATCGGGAACCTTTGATCTTCAATATAGTTACAATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTTGGGTATAACAGGATGAGGAGGACGATTCGAAGTCACGATCATGCGCCCAAGTCAGAATGACTCCACACTACTCCTCCTCAGGACCATTTATAAATAAACAGTGATCAAGATTCCAACAATTAAGATGGCTTGAAACCAATTTCTGCTCTTGTTTTTGTTCCCACTCCCCCCTCCCCCCGAGGTCAGGATGAAGTATTAACTCTGAAGATAAAGGACCCCACGACGACAACGGCTTCCAGTTACTTCGAAGGCATTTTTCTACTTCTACTTCCCCTCCGTCTCATCCTCCTCCTCAGCTACCAAATTCACAATAGGACCGCAGGAAAAGTCTGTAGCGAATAGAACCTTCTTCACTACGGTTTCGTACCTAAAATGTTCTGGAAAAATGGATAGAAAAGAATCTTTTAAAATCGAAATCCGATTTTCGGAGTGTTAACAATGTAACTGTTGTAGAAAAGGAGCGGTAAATGAGACGTGGGGAATAAGATACAGAGCAACCACTGTCGTTAAGGACCGTTTGAGTGTTT +>2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_template CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 +GTATTTCTTATGATATTAGATGTAGGCTGGAAATAGAATGCGTGCTTTACAGGCCTCCTCTGCGTATGTTTCCATGGAAGCCGTAGGAACCTTTGATCTTCATACTTGCCCTATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTGATATAACAGGATACGGAAAGAGTTCGAAGTCGAATCGTCCAGCAAGTCGAATGACTCTAAAGACATCGGCACGGCCTTTGAGGCTCGTATATGCCTAATTCCAACAATGCAAAGTACGTGGAACAGATTTCTGCTCTTTTTTGTTCCACTCCGCCAGCCCCCCGAGGTCAGGATGAAATATTACTCTGAAAACCGCCAACCCACGGGACAGCTACGTCGAATGTCGTCGAACAGTTCTATTCCTTCCCCTCCGTTAGTACTACTCTAGGCTACTCAATTCAGGCGATAGAAGGAAAAGTCTGTACCAGGCGGGTTCTTCGGCTTTTCAATGCGCGCTGTTCTGGGGAGCTATCGCTGCAAAGAATCTTTTAAAATCGAGTCGAGTTTTCAGAGTGTTCCTCAATGTAACTGTTGGCAAAGGAGCGGGCCTGGCAGACGTGGGGAATAAGACCCCAAAACCACTTCGTGCACATCGTTCTGGTGTTCATCTGTTCTTAGCTCTTGT diff --git a/tools/poretools/test-data/poretools-winner-out2.tabular b/tools/poretools/test-data/poretools-winner-out2.tabular index 0e759ce8aff..4152bfa0d53 100644 --- a/tools/poretools/test-data/poretools-winner-out2.tabular +++ b/tools/poretools/test-data/poretools-winner-out2.tabular @@ -1,2 +1,2 @@ ->2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_2d CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 -CATGTTTCTGCTGATATTGCTAATGGCTGAACTGGAAATAAGGATCCGTTGCTTGCCAACAACTATACTGCGTGGTATTTTCCCAGTGGAAAGATCGGGAACCTTTGATCTTCAATATAGTTACAATTGGTGGTCGTGATTTTAATCCCAGTTCATCCTTATTTTGGGTATAACAGGATGAGGAGGACGATTCGAAGTCACGATCATGCGCCCAAGTCAGAATGACTCCACACTACTCCTCCTCAGGACCATTTATAAATAAACAGTGATCAAGATTCCAACAATTAAGATGGCTTGAAACCAATTTCTGCTCTTGTTTTTGTTCCCACTCCCCCCTCCCCCCGAGGTCAGGATGAAGTATTAACTCTGAAGATAAAGGACCCCACGACGACAACGGCTTCCAGTTACTTCGAAGGCATTTTTCTACTTCTACTTCCCCTCCGTCTCATCCTCCTCCTCAGCTACCAAATTCACAATAGGACCGCAGGAAAAGTCTGTAGCGAATAGAACCTTCTTCACTACGGTTTCGTACCTAAAATGTTCTGGAAAAATGGATAGAAAAGAATCTTTTAAAATCGAAATCCGATTTTCGGAGTGTTAACAATGTAACTGTTGTAGAAAAGGAGCGGTAAATGAGACGTGGGGAATAAGATACAGAGCAACCACTGTCGTTAAGGACCGTTTGAGTGTTT +>2f378243-7a3f-4584-bfb6-6800def37547_Basecall_2D_complement CPHG_CNU4299G4G_louse_library_2016_3_4_3507_1_ch126_read326_strand .poretools_tmp/test-data/2016_3_4_3507_1_ch126_read326_strand.fast5 +ACACTAGCATCTGTCTGGCCCCGATATTTGTAGTATGTACTTTACGTGTACTGTTACTATGGTATTTTCACCCTCAGTTTGCCCTTGTCACTCGAAAGTCGAATTCAGTGTTTTAAAAGATTGTCTGGTTCTATCGGTTCCGAGCAGTTTTAATAGAACTGATCAATGAAGAAGGTTCGTTCGAGCGAACTTCCAGTGATCTTGTGAATTTGAGCTGAGGAGGAGATGAAAGAGGGAAGTAGAAGTAGAAAAATTGCATCGAAATATGGAATAAATTGTATCGTCGGTCTTGCTTTTATCTGTCAGTTATACTTCAGTAGGAGGGAGTGGGATAACGACAGCAATTAGTTCAGCCTTAGTGTTGAGGAATCTGGTTCTTTAACATCTTTGGTGGGAGGAGTGTCCTTGATTTAATATGCAGAAGTATCCTTGCTGCGAATCGTCATCATCCTTTAACAATAGGATGAAAACCGTTAAAATGCCGACAGTTGGACCTGCGAGCCGCCGGCCCGTATTCATGGGAAAGTACCGCATTAACGTGTGTCAGGCGGGACGTATTATTTCCCGTTCAGCCGATTAAGTATACAGGCACAGAGACTTCC From 3d29c24dd45a3d69b784c8b5762d357eda4a4a7f Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 13:13:23 +0200 Subject: [PATCH 16/36] improve docstrings --- tools/idr_download/idr_download_by_ids.py | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index bd7d42e6264..465f045fb24 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -15,9 +15,9 @@ def warn(message, image_identifier, warn_skip=False): - """Print an error message to stderr and - - prefix with the image identifier - - suffix with 'Skipping download!' if warn_skip is True + """Print an error `message` to stderr and + - prefix with the `image_identifier` + - suffix with 'Skipping download!' if `warn_skip` is True Args: message (string): Message to print to stderr @@ -39,7 +39,7 @@ def warn(message, image_identifier, warn_skip=False): def find_channel_index(image, channel_name): - """Identify the channel index from the image and the channel name + """Identify the channel index from the `image` and the `channel_name` Args: image (omero.gateway._ImageWrapper): image wrapper on which the channel should be identified @@ -66,7 +66,7 @@ def find_channel_index(image, channel_name): def get_clipping_region(image, x, y, w, h): - """Check x,y and adjust w,h to image size to be able to crop the image with these coordinates + """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates Args: image (omero.gateway._ImageWrapper): image wrapper on which region want to be cropped @@ -109,7 +109,7 @@ def get_clipping_region(image, x, y, w, h): def confine_plane(image, z): - """Adjust/Confine z to be among the possible z for the image + """Adjust/Confine `z` to be among the possible z for the `image` Args: image (omero.gateway._ImageWrapper): image wrapper for which the z is adjusted @@ -128,7 +128,7 @@ def confine_plane(image, z): def confine_frame(image, t): - """Adjust/Confine t to be among the possible t for the image + """Adjust/Confine `t` to be among the possible t for the `image` Args: image (omero.gateway._ImageWrapper): image wrapper for which the t is adjusted @@ -147,7 +147,7 @@ def confine_frame(image, t): def get_image_array(image, tile, z, c, t): - """Get a 2D numpy array from an image wrapper for a given tile, z, c, t + """Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t` Args: image (omero.gateway._ImageWrapper): image wrapper from which values are taken @@ -171,7 +171,7 @@ def get_image_array(image, tile, z, c, t): def get_full_image_array(image): - """Get a 5D numpy array with all values from an image wrapper + """Get a 5D numpy array with all values from an `image` wrapper Args: image (omero.gateway._ImageWrapper): image wrapper from which values are taken @@ -232,7 +232,7 @@ def download_image_data( - a 2D cropped region or - a hyperstack written in a tiff file - the original image uploaded in omero - Optionally, th final file can be in a tar + Optionally, the final file can be in a tar Args: image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-' @@ -546,7 +546,7 @@ def download_image_data( def _center_to_ul(center_x, center_y, width, height): - """Convert the center coordinates, width, height to upper left coordinates, width, height + """Convert the center coordinates (`center_x`, `center_y`), `width`, `height` to upper left coordinates, width, height Args: center_x (int): x coordinate of center From 03ed6ceb3d222f1059e96823ecc51a9290662ece Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 26 Sep 2024 13:34:12 +0200 Subject: [PATCH 17/36] add more lineargap examples to axtchain --- tools/ucsc_tools/ucsc_axtchain/axtchain.xml | 27 +++++++++++++++------ 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/tools/ucsc_tools/ucsc_axtchain/axtchain.xml b/tools/ucsc_tools/ucsc_axtchain/axtchain.xml index ebcf2c838fd..06a15410cb6 100644 --- a/tools/ucsc_tools/ucsc_axtchain/axtchain.xml +++ b/tools/ucsc_tools/ucsc_axtchain/axtchain.xml @@ -72,17 +72,28 @@ `axtChain`_ is a tool to chain together alignments in `axt`_ format. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously. +For implementation details see axtChain's `source code`_. -sample linearGap file (loose):: +linearGap defaults: - tablesize 11 - smallSize 111 - position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 - qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 - tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 - bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 +loose:: + + tablesize 11 + smallSize 111 + position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 + qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 + tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 + bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 + +medium:: + + tableSize 11 + smallSize 111 + position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 + qGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 + tGap 350 425 450 600 900 2900 22900 57900 117900 217900 317900 + bothGap 750 825 850 1000 1300 3300 23300 58300 118300 218300 318300 -For implementation details see axtChain's `source code`_. .. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt .. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html From f3b73864fc34568226f758ef617ff124162692a0 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 13:34:23 +0200 Subject: [PATCH 18/36] add typing --- tools/idr_download/idr_download_by_ids.py | 78 +++++++++++------------ 1 file changed, 39 insertions(+), 39 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 465f045fb24..963dc0e94b0 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -10,11 +10,11 @@ import numpy from omero.cli import cli_login from omero.constants.namespaces import NSBULKANNOTATIONS -from omero.gateway import BlitzGateway +from omero.gateway import BlitzGateway, _ImageWrapper from tifffile import imwrite -def warn(message, image_identifier, warn_skip=False): +def warn(message: str, image_identifier: str, warn_skip: bool = False) -> None: """Print an error `message` to stderr and - prefix with the `image_identifier` - suffix with 'Skipping download!' if `warn_skip` is True @@ -38,11 +38,11 @@ def warn(message, image_identifier, warn_skip=False): ) -def find_channel_index(image, channel_name): +def find_channel_index(image: _ImageWrapper, channel_name: str) -> int: """Identify the channel index from the `image` and the `channel_name` Args: - image (omero.gateway._ImageWrapper): image wrapper on which the channel should be identified + image (_ImageWrapper): image wrapper on which the channel should be identified channel_name (string): name of the channel to look for Returns: @@ -65,11 +65,11 @@ def find_channel_index(image, channel_name): return -1 -def get_clipping_region(image, x, y, w, h): +def get_clipping_region(image: _ImageWrapper, x: int, y: int, w: int, h: int) -> list[int]: """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates Args: - image (omero.gateway._ImageWrapper): image wrapper on which region want to be cropped + image (_ImageWrapper): image wrapper on which region want to be cropped x (int): left x coordinate y (int): top y coordinate w (int): width @@ -80,7 +80,7 @@ def get_clipping_region(image, x, y, w, h): ValueError: if the x or y coordinates are larger than the width or height of the image. Returns: - list of int: new x, y, width, height adjusted to the image + list[int]: new [x, y, width, height] adjusted to the image """ # If the (x, y) coordinate falls outside the image boundaries, we # cannot just shift it because that would render the meaning of @@ -108,11 +108,11 @@ def get_clipping_region(image, x, y, w, h): return [x, y, w, h] -def confine_plane(image, z): +def confine_plane(image: _ImageWrapper, z: int) -> int: """Adjust/Confine `z` to be among the possible z for the `image` Args: - image (omero.gateway._ImageWrapper): image wrapper for which the z is adjusted + image (_ImageWrapper): image wrapper for which the z is adjusted z (int): plane index that need to be confined Returns: @@ -127,11 +127,11 @@ def confine_plane(image, z): return z -def confine_frame(image, t): +def confine_frame(image: _ImageWrapper, t: int) -> int: """Adjust/Confine `t` to be among the possible t for the `image` Args: - image (omero.gateway._ImageWrapper): image wrapper for which the t is adjusted + image (_ImageWrapper): image wrapper for which the t is adjusted t (int): frame index that need to be confined Returns: @@ -146,18 +146,18 @@ def confine_frame(image, t): return t -def get_image_array(image, tile, z, c, t): +def get_image_array(image: _ImageWrapper, tile: list[int], z: int, c: int, t: int) -> numpy.ndarray: """Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t` Args: - image (omero.gateway._ImageWrapper): image wrapper from which values are taken - tile (list of int): [x, y, width, height] where x,y is the top left coordinate of the region to crop + image (_ImageWrapper): image wrapper from which values are taken + tile (list[int]): [x, y, width, height] where x,y is the top left coordinate of the region to crop z (int): plane index c (int): channel index t (int): frame index Returns: - numpy array of 2 dimensions: image values of the selected area + numpy.ndarray: image values of the selected area (2 dimensions) """ pixels = image.getPrimaryPixels() try: @@ -170,14 +170,14 @@ def get_image_array(image, tile, z, c, t): return selection -def get_full_image_array(image): +def get_full_image_array(image: _ImageWrapper) -> numpy.ndarray: """Get a 5D numpy array with all values from an `image` wrapper Args: - image (omero.gateway._ImageWrapper): image wrapper from which values are taken + image (_ImageWrapper): image wrapper from which values are taken Returns: - numpy array of 5 dimensions: image values in the TZCYX order + numpy.ndarray: image values in the TZCYX order (5 dimensions) """ # The goal is to get the image in TZCYX order pixels = image.getPrimaryPixels() @@ -209,23 +209,23 @@ def get_full_image_array(image): def download_image_data( - image_ids_or_dataset_id, - dataset=False, - download_original=False, - download_full=False, - channel=None, - z_stack=0, - frame=0, - coord=(0, 0), - width=0, - height=0, - region_spec="rectangle", - skip_failed=False, - download_tar=False, - omero_host="idr.openmicroscopy.org", - omero_secured=False, - config_file=None, -): + image_ids_or_dataset_id: str, + dataset: bool = False, + download_original: bool = False, + download_full: bool = False, + channel: str = None, + z_stack: int = 0, + frame: int = 0, + coord: tuple[int, int] = (0, 0), + width: int = 0, + height: int = 0, + region_spec: str = "rectangle", + skip_failed: bool = False, + download_tar: bool = False, + omero_host: str = "idr.openmicroscopy.org", + omero_secured: bool = False, + config_file: str = None, +) -> None: """Download the image data of either a list of image ids or all images from a dataset. The image data can be: @@ -235,14 +235,14 @@ def download_image_data( Optionally, the final file can be in a tar Args: - image_ids_or_dataset_id (list of string): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-' + image_ids_or_dataset_id (list[str]): Can be either a list with a single id (int) of a dataset or a list with images ids (int) or images ids prefixed by 'image-' dataset (bool, optional): Whether the image_ids_or_dataset_id is a dataset id and all images from this dataset should be retrieved (true) or image_ids_or_dataset_id are individual image ids (false). Defaults to False. download_original (bool, optional): Whether the original file uploded to omero should be downloaded (ignored if `download_full` is set to True). Defaults to False. download_full (bool, optional): Whether the full image (hyperstack) on omero should be written to TIFF. Defaults to False. channel (string, optional): Channel name (ignored if `download_full` or `download_original` is set to True). Defaults to None. z_stack (int, optional): Z stack (plane) index (ignored if `download_full` or `download_original` is set to True). Defaults to 0. frame (int, optional): T frame index (ignored if `download_full` or `download_original` is set to True). Defaults to 0. - coord (tuple of int, optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0). + coord (tuple[int, int], optional): Coordinates of the top left or center of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to (0, 0). width (int, optional): Width of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0. height (int, optional): Height of the region to crop (ignored if `download_full` or `download_original` is set to True). Defaults to 0. region_spec (str, optional): How the region is specified ('rectangle' = coord is top left or 'center' = the region is center, ignored if `download_full` or `download_original` is set to True). Defaults to "rectangle". @@ -545,7 +545,7 @@ def download_image_data( raise -def _center_to_ul(center_x, center_y, width, height): +def _center_to_ul(center_x: int, center_y: int, width: int, height: int) -> list[int]: """Convert the center coordinates (`center_x`, `center_y`), `width`, `height` to upper left coordinates, width, height Args: @@ -555,7 +555,7 @@ def _center_to_ul(center_x, center_y, width, height): height (int): height Returns: - list of 4 int: x, y, width, height where x,y are the upper left coordinates + list[int]: [x, y, width, height] where x,y are the upper left coordinates """ if width > 0: ext_x = (width - 1) // 2 From 902d6f92b38836abf76b5a8a6f7cc5b8fa47c3cf Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 13:35:19 +0200 Subject: [PATCH 19/36] run black --- tools/idr_download/idr_download_by_ids.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 963dc0e94b0..2892df4ebe8 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -65,7 +65,9 @@ def find_channel_index(image: _ImageWrapper, channel_name: str) -> int: return -1 -def get_clipping_region(image: _ImageWrapper, x: int, y: int, w: int, h: int) -> list[int]: +def get_clipping_region( + image: _ImageWrapper, x: int, y: int, w: int, h: int +) -> list[int]: """Check `x`, `y` and adjust `w`, `h` to image size to be able to crop the `image` with these coordinates Args: @@ -146,7 +148,9 @@ def confine_frame(image: _ImageWrapper, t: int) -> int: return t -def get_image_array(image: _ImageWrapper, tile: list[int], z: int, c: int, t: int) -> numpy.ndarray: +def get_image_array( + image: _ImageWrapper, tile: list[int], z: int, c: int, t: int +) -> numpy.ndarray: """Get a 2D numpy array from an `image` wrapper for a given `tile`, `z`, `c`, `t` Args: From c255347182d5877e32997c8189a86479a08aee30 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 13:36:24 +0200 Subject: [PATCH 20/36] fix warn I introduced --- tools/idr_download/idr_download_by_ids.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 2892df4ebe8..70b7c8ff9c3 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -205,8 +205,7 @@ def get_full_image_array(image: _ImageWrapper) -> numpy.ndarray: ) except Exception as e: warning = "{0} (ID: {1})".format(image.getName(), image.getId()) - warn("Could not download the requested region", warning) - warn(e.msg) + warn(f"Could not download the full image \n {e.msg}", warning) return return all_planes_reshaped From edceaaff2891854d44bb42344533b3c5d07e3338 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 26 Sep 2024 13:41:14 +0200 Subject: [PATCH 21/36] fix linting --- tools/idr_download/idr_download_by_ids.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/idr_download/idr_download_by_ids.py b/tools/idr_download/idr_download_by_ids.py index 70b7c8ff9c3..bae7da3a5ec 100644 --- a/tools/idr_download/idr_download_by_ids.py +++ b/tools/idr_download/idr_download_by_ids.py @@ -10,7 +10,7 @@ import numpy from omero.cli import cli_login from omero.constants.namespaces import NSBULKANNOTATIONS -from omero.gateway import BlitzGateway, _ImageWrapper +from omero.gateway import _ImageWrapper, BlitzGateway from tifffile import imwrite From e3b506ea64f57aef2d05073d2481047a772aa529 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 26 Sep 2024 14:10:02 +0200 Subject: [PATCH 22/36] add more parameters to ucsc axttomaf plus new test --- tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml | 44 ++++++++++++++++++- .../ucsc_tools/ucsc_axttomaf/test-data/2.axt | 19 ++++++++ .../test-data/hg38.noprefix.fasta.fai | 24 ++++++++++ .../test-data/mm39.noprefix.fasta.fai | 21 +++++++++ 4 files changed, 107 insertions(+), 1 deletion(-) create mode 100644 tools/ucsc_tools/ucsc_axttomaf/test-data/2.axt create mode 100644 tools/ucsc_tools/ucsc_axttomaf/test-data/hg38.noprefix.fasta.fai create mode 100644 tools/ucsc_tools/ucsc_axttomaf/test-data/mm39.noprefix.fasta.fai diff --git a/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml b/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml index fffe3758e92..537e5688bc0 100644 --- a/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml +++ b/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml @@ -1,9 +1,21 @@ - + Convert dataset from axt to MAF format 469 + + + + + + + + + + + + UCSC_Genome_Browser_Utilities @@ -25,6 +37,14 @@ #else: '$query_reference_index_source.que_ref_index_file.fields.path' #end if + #if str($t_prefix) + -tPrefix='$t_prefix' + #end if + #if str($q_prefix) + -qPrefix='$q_prefix' + #end if + $score + $scoreZero '$out' ]]> @@ -60,6 +80,14 @@ + + + + + + + + @@ -77,6 +105,20 @@ + + + + + + + + + + + + + + diff --git a/tools/ucsc_tools/ucsc_axttomaf/test-data/2.axt b/tools/ucsc_tools/ucsc_axttomaf/test-data/2.axt new file mode 100644 index 00000000000..c88ac3f3ad8 --- /dev/null +++ b/tools/ucsc_tools/ucsc_axttomaf/test-data/2.axt @@ -0,0 +1,19 @@ +0 chr1 52448 53340 chr2 111209343 111210259 + 33103 +GCCAATGGATAGAGTAAATAATTCTGCGGTATCTAAATTTGTATTGATTGGACTTTCAAGCTCTTGGGAGATGCATCTTTTTCTTTTTTGGTTCTTCTCTGTGTTCTACATGGGAATTATCCTGGAAAATCTCTTCATTGTGTTCACAGTAATTATTGACTCTCATTTA-AATTCCCCAGGTACTGCCTACTGGCCAACATTTATCTTCTTGATCTGGG----TCTTCTCCTACAGT-------------TCTGACTTTTTCACTAACTGCAGCATCATTTCTTTTCCAAGATGCATCATACAGATATTTTTCATTTGTGTCATGCGTAAAAATTGAGATGGTGCTGCTCATAACCATGGCATAGAGCAGGTACACTGCCAATCTGTAAGCCTCCCCATTACCTGACCACAATGAACCCCAAAATGTGTGTTTCCTTTGT---TGGAGGCATCCTGGATAGTCAGGATAATCCATGCTGTATCTCAGTTTGTTTTTGCCATAAACTTGCCTTTTTGTGGCCCTAATAGAGTAGGTAGTTTTCACTGTGATTTTCCTTATGTCATGAAACTTGCTTGTGTAGACACTTACAAACTAGAGGTTGTAGTCACTGCTAACAGTGGGCTTATATCCATAGCTACCTGTTTCTTATTAATAATATCCTATATTTTCATTTCGGTAACCGTCTAGAATCCTTCTTCAGGAGACTTATCTAAAGCATTTGT-GTCATGTTAGATCACATCACAGTAGGGATTTTGTTTTTTATGCCATGTATATTTCTGTATGTGTAGCCTTTGCCTAAAACAACACATGATTAATATTTGTTCATTGTTCCTTTTGCTATCACCCCTG--------TCTAGGATCTACACATTAAGAAACAAAGACATGAACGTCTCCATGGAAAGACTGGGAAAATGGA +GTCAATGGATCAAATAAATGAAACTGTAGCTTTTGAATTTGTGTTGTTGGGACTCTCCAGTTCTTGGAAAAATACAATTTTTCTCATGTCCACCTTCTCTTTGCTCTATGTAAGCATCATCGTGGGAAACCTTTTCATTGTCTTTTTGGTAATTAATGACTCCCGTTTACAGTCTCCTATGTATTTTCTTTTGGCCAATCTGTCCCTCATTGATGTTGGACTTTCCTCTACCACAGTGCCCAAGATGATCTCAGATCTTCTGAAAGAGCACAAAGTAATATCTTTCCACAGTTGCATGACTCAGATCTGCTCCATCCACATTATG-GGAGGAGTGGAGATGGTGCTGCTCATAGCCATGGCGTTTGACAGGTACACGGCCA-TCTGTAAGCCTCTGCACTACATGAGCATCATGAGCCCTAGAATATGCATTTCATTTGTAATTGCTGGC----TGGGTCACTGGAGTGGTCCATGCCATGTCACAGTTCTCTTTTGTTGTGAACCTGCCTTTTTGTGGTCCTAACAAAGTGGACAGCTTTTACTGCGACTTCCCTCGAATCATACAACTGGCATGCACGGATAGAGACACATTTGAGTTTGTTGTTGCTGCCAACAGTGGCTTCATGACCTTGGGGACCTTCTTCTTGCTTCTCCTCTCCTATGTCTTCATTTTGGTCACAGTCTGGCAAAGGTCTTCAGGGGACTTGTCAAAGGCGCTTGTCACTCTGTCAGCTCACATCACTGTGGTTGTTCTGTTTTTTACTCCATGCATGTTTCTCTATGTGTGGCCTTTCCCCACATCATCGACTGACAAATACCTGTTCATTGTTGACTTTGCTGTCACCCCTGCTCTTAATCCTGTCATCTATACTTTAAGGAACAAAGATATGAAGGAAGCCATAAAAAAGCTGAGCAAGCAGA + +1 chr1 56555 58924 chr2 111303515 111305845 + 43395 +CACATTATTCTGCAGTTTTTATCTTGCTTACGTATTTTTGGAATGTTACTATTTTTCAAAAATTAATTTGGGATCAACCAACACTTCTTATTCTGCTGCTGTTCTAGAGAAAATCATTTTCCTCATTTCTGAACAAGAGAAAATGAAAT-----------------ACAGCTCTAAACAAATGCCACTGTAAACCAAGGTGGAGCCTTTGCACTTTCAGGCCACCATGATAACCT---GGAGATTAGATTTTTCTGTGTCTTTATATCAATAATAAAGCCAAGCTTCTCCAGGGGTATCCACTAGGCTTGTCTCAATGGCTCAATACAGGTCCTTTTGTGAATGATTACCTCACCCTCATGGAAACACACTCTT-GTTACAGAAACTCAGAATGATTCTATTTTTTCTTTTATATTTGTATATGTTTTTCCAATACCTCTGAAAAAACTGATCCAAAAAAAATACAAATTTTAATTGTAGCCAGTCAATTCAGGAAGGATAAAGGTCAAAAACTTTCAAAGAAACCTTCAGCCCCAACACACTAAACTTTGGGAGCACAGGTTGGCATCCAGAGGTAAACATTTGCTATAACTGATAACAGGAGAAGGATCCATTTATTCACCTGTTATCAATTACAGGCATTGTATTTAAAGATCAGATGTTTTATATTTATTTCTTCAAATTTCATTCATGGTGCCATAAGTGAAGGTATCTCTGTCCACCCTGAATATATTTTCACTCCCTCATCTCAGTCATTCCGAACAATTCACACACTAAGATTACCCATGCTAAATGGGGATTCTTTTTTACTAGCCAATGTAGTACCTCAAATCCTTCCTTCCCTCCCCCTATTTCATCAGCAGGCAATTCTTTTGATACTTTTGTCAAGGGGAAATTGTGTGACTCAGAGATCTAGTCCCCAAGAGAAACTAATAATGGGCTGGGTATTGTCTGTCTCAGCAGCATCAGTGGGTCCCTCTCCTGTGCAGCTAATTAGCTTCCTTTCCAATATGAAGAATCTTATATATAGCTTTGTCTTT-GGGGTATTAC----ATAAATGAAGATTAAGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGCTTTTAATTACAAAACTTTCCCTGTCGTGGTTGCTTCTCTCTATCCTTCTAAACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTT--ATCTTTTTCTTCCACACTATCTC----TTATTTTCCAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAACCCCTATGATA--ATTTCAGTTTG--TCCCTAGTATGAAG-TTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTAATTATAAACTTCATTTTCCACTCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCAGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTATCTC-AGATTCAGAAAGATTTGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGACTATGAATTC--TGAAATGGAACTGTTCCAG-------------GTTGAAGAAATAAGAAAGGGAATTGGGAAGAGCAAT-----GCCCAGTGAAAAAGAAGAAATAA-TATTTTAGGAAGT-GAATGC-TAATTTTATTTTAAACAAAATAAGAACTCAAGGAATAAGAGGGTTCTTCCAATAGGTTAGAGTGATCCTGTCAAACATATATGCTTCT-AGATTTTTTTAAAGACTGTTTCTACTAAGAAAGCATAGACCGCTATTGAGAAAGATCATTAAACTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATTGTTAGCCAT----TTAACCACACTGTGTTGTTTC--------TCA--TTCTACCTGTAGAATCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAA--GATATGTGTCCC-AGACCCTAAATGACTGACAAATTTTAAATCTCC---AATAGGAAAGATGACAAACTCTATGGAAACTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACAC-----------------------------------ATGG----------------------------TCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATA---AAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTT +cacattgtattgta--ctctattatgttt-tattgtattatattatTGTTGTTTTTCAAAAATT----TTGGTTAAACTAGCATCCCTTCTTTTTCTGTTGACCTAAGAAGAAACCCTTTCCTTCTTT-TGAACAAGATAAAATGAAGTGCAGATTTCTAAACAACACAGCTTTAAAGAAGCACACTTATAAACAAAGGTAGAGCTTTCACTGTTTCA-------ATGA-AACCTCAGTGAGATCAGATT-----ATGACTCTACATAAATGACAAAG------------------ACCCACCGAGACTGGTACCATGTTTTCATTCATATGGTGTTA--AATGATGGTCTC---CTCGGGTATCCAGACCCTTCATTTAAGTAACTCAAAACAACT----------------ATCTATAT-----CTTCCAAAATTTCTAAACAAATTGACCCGATGACT-TACAAGTTTAACTTATAATAGATCAACTCA--AATGATAAAA--TAGTGATTTTCAGATATACCTATATCCTCTGG---------TTTTGTAGAGCATTCAGGCTTTCTTGGACAAACATTTGTCA-AAATGA-AACAATAAGAACTTTTATCTTTTTCCATACTAACAAGTGAAG----TGTATTTTCAGATAATTAGTTTTAGACT-ATTTTT---AATTTGATATATGAATCCA-GAGTAAAAATACAGCTATCCACTTTTGGAATATTTTTTATTCT-----------ATTTCAAGCAATTCATAAAAAAAGATTATAACTCCTCAA-GGAGGTTATTTTAAATT---TAATACATTACACAGAATATTTTTATTTTTTCCCTT-TTATATAACCAGACAATTCTTTTGATACTTCTCTCTTGGGGAAACCA-ACAGCTCAT-GATCCAATTCCCAATAGAAACTATTAATGAACTGGGTATTGGACACCTTCACAGTGCCAATGGGTCACTCTCCTGAGCAAATAATTGGCTTCTTTGCCACTATAAACAGTCATACATATATCTTTGTCTTCAGGGGCATTGCTTATAGAAATGAATGATAACCTACTTAAATTT-TCTTTTTCTTCAAAGCGTACCTGCTGTTACTTTAGAGA-AGGT--AAGGGGTGGTTTACATTTAAAACCTG--CCGATTATAGTTG----TTTCAATCTTGCTAA------CTCTAAT---CTCCCATCTGTAAAATAATTATGTCAGACAT-GTCACCTTTCAAGAGTATTTTTACCCTTTTAATTTTAAACTATCACAGAATCGTTTTGTGATTTTATTTA--AAAATAT----TGCTTTATATAATTAATCTCGTGCTCACAACCTTTTGATATTTTTTTAATTTGCTTCTTTGGTATGAAGATTTTTCAAGAACGTGTG--TTTCTGCTTTTTGTAGCCCTCAGACAATTGTGCAATTCATTTCCAACTATGCCAAGCAGATGTCTGGTCTCAGATATTTCCTGCATA-TTAAAGATCATATTACAATCTCAAT-----------AATCTCAAGCCTTGTCTGCCAATACTCTGGAGTAATTCTTACCTTT----TATT-------TCAATATTTGAATACTGTAAGCAGTGAATACACTGAGAGACTATTCCAAGACTTAGATATATT-----CTAGCCCACAGGATTCTAAAAAAGTGC-ATTAAATAGAAATTCTTTTTATTGCAACTGTTCAAGTAGTGGTCTAGATGTTTGAAAAA-AAGAAAAAAAATTGGCAAAGTCTATTAAGGGCACAGGGTAGGGAAAGGACTAGTTTTTTTACGAAGTAGGATGTGTAGTTTTATGCCAAACTGAGTATGAGTTCAAAGACTAACACAATCCTTTCAGTAAAGCAAAGTGATCATATCAAATATATAGTATTCTGAGATTTT----ACAACTGTTTCTCCTAATCATTTGTAGAGTAATACTGACGAA---CAGTACACTAGAGTTTAGGACACCTACCCTCTGA-TCTGTAGTTCTGTATGTTTTGCTCTTGATGCTGTTAA--ACACTAGGCTGTTTTATGCAGAATCAAGTGTTAAATGCGTTTTCTCACAGTTGTTCCCAGTTTTCATGTAAATCTACGATTCCATTAGTATGCTTTGTTTAACACATGTCTATGTATCTTGTTTGAAGTGATACTTATCCCTAGACCTTGAATAATAGACAAATTTTAAGTCACCACAACCAGGAAAACCATCAAACACTATGGGGACTTGGTTTCTGATGCACTCCTTGAAGCTCCATGCTGTTATCAACAGCTCT---GAAGGGAAAGGAATAAAGCACTATattttgcttttgttttgattttatattttgaGATGGAGCTGAGAAGTTGTTTTGTTGTATTTTTACTATTTTTACACATAAATTCTCTAGAAACATGTGGATTtaat-aataatatataaaaataataaCCCAAAATGCTTGTAA-------GATAAAAAGACCTTCATTTATTTAAGTTCTCATTCTTT + +2 chr1 60917 61125 chr2 111306441 111306644 + 8501 +TTAATATTTCCCACTTCATCATTACTAACCTCACTCACTCTGAACTTGATGAGAGCACCTGAGCATTAATTTTTCTTATAATTATTTAATGATTACCAGAATTCGTTCAGTATGGCCAGCTCTGGTCAAAGTGAGGCAGGCAAGATGCTTTGTCAACTGCCTGGATGGAATGTCTCAAAAGGTTTCCATTTCATGGTAGCATTATGCAA +ttAATAT--CCCAGTGCACC-TCACTACTCTGGCTCACGCTGAGCCTGATGAGGTCATA-GGGCATCCATTTTTCTTGTAGTTATTTTATTATTACCAGAATTCATTCAGAATGGCCACCTCTAGTCAACACAAAATAAGCAGCGTGCTTTGTC-ACTATTTGAGTAGACTTCCTTAGGAAGTTTTCATCTTAGGGTAGTTTTACATAA + +3 chr1 61126 61836 chr2 111307411 111308031 + 9500 +AGTTCAAGACGTTTAATCAAGACCCTTCACTTACTTAACTATACCTCCTTGAGA-ATCCCATCTATGAAAAAATTCTAGTCATTATAAAAATGATTGATTAAATGAGGGAAGTAGTAGAGTTCTTCATTTCTTTAGTTGGTTTAGTCTCCTATGAGTCAATCCTA-TTTTCAAA-ATTCTTAATAAACCATTTATTCCTTCAACTTTCTATGCCATTTGATGTTTTGTAAAAAAAAAAATATAA------TATGTATACAAAAAGATATTTCAAAATCTAGAAAGAGAGCTTTAGAGCTTTGTAAAGCTCTTTTAAAAATCAAAAACAACTACTGTTAATTAACATGTTGTACTATGC-AATTTGTTTACCATTATTACTCTTGGTATTTTTAAGAAAAGTCTT----TCCATTGTTATTATAAATGCTTCTATTGATATTTATTTTAATAACTGTTATTACAGTCCGTCATGTACATACACTATACTTAAAcctaatgtttggtatttaaatcgtttcaagattttatc----actgtcaacaaagtatgatgaatattttta--tgctgaaaacttctgtaaaaatagaattccaagagtattattgcaccaaaaggcatggacttaaaattcttgatacatgatttcaaaatattttctttaaggtttgaatcagtctatattccctccagcagcgtataaaagtgccaatttctctgatccttagcc +aGCCCAAGAAAATTAAACAAATCCCTTTACTAATTTAAATGTATCTTGCTACTAGATATCATTTGTGA---------------CATAAATATTTGCAATAAAAT--------CACTAACATTATTTATTTCATCAGTG-------------ATGGGTTAACCCTAGTTTTCAAACAGCTTTGATAAATCTGTCATCTCTTTAGATCACTAGATAATTTGATATTTGAGGGGAAAATAGATATGAATGCACTATGTGCATTAAAATATCCCTTAAA-TCTAAAAATAGAA-TTAGAAGCTCTG------------AAACCTGAAATGCTATCATTGTAACCGGGAATGATGGGATATGCTAATTACTTTACAACAAT----------GTTTTAAGCAAGAATCTTAAAGTCCA------------------------ACATCTAGTTT------TGTTATTATAGCCAACTGTGTATATTTGATATATTTATACCTAATTGCTTTCATTTAAACTGCCTTAAAGCTTTACTTAAAACTATCAATAAAGTCTTGCTAGTATTTGTGACTGGAGATATTATCTGTACAAGTAGTTATTTCAGAGAAGTACTTTACAACAAGGTATGGAGATAAAATTATTGACATAT---------------TGTTTAAGGGTTAAA-----ATATCTTCCCTCTTGTGAATTATAAATAAACCAATTTCATTGAGCTTTTGCT + +4 chr1 61944 64435 chr2 111308032 111310602 + 69061 +ctccgcctcccggggtcaagctattctcctgcctcagcctcccaagtagctgggactacaggcatgcaccaccatgcccagctaatttttgttatttttagtagagatggagtttccccatgttggacaggatggtctcgatctcttgacctcgtgatccaccctcctcggcctcccaaagtgctgggataacaggcgtgaacaaccatgcccggcctgtaaaactttttcctaatttaacagaaaaataatagtattatattttatcatatttctttgatttctaAGacacacatacacacaca---cacacacatatctgtatatacaaatacacgtatagc---------------------------------------------ttacaTTTT--AATTCTTCATTTCATTTGTTCATTTATTAGGTCTTGGAGATTTTGTGAAAC---------TGTTTAAATTCTTTTTTATACTATGAAGATATCAACCTT-TTGTCTCTACAGCATTTCAAATTCAAGTATGAT----TCACGTGTTGGTTTGGGGTAGATCATTATAGGCACATGTAGGAAACAGCTTT-----------------------------------------------------------------------CAGAGA----------------TGC----------CTTAACCGT-----------------------------------AATTATGCATTTGTATTC--------------TAATTTTTATTTAATGTTATTATT----GATTGCATTTTTAAAG--ATTCTGT--ATTTTTTAAACCATTTATTTGTATATGTTGGTATACAATCTTGCCATTTTCTGGGATTTCATATTTCCTTATTTTTGTTTTT--TACCTTTTTTGGCTTGAATT---TTTTGAGTTTTTATGCATTCTTTTCCAGTTTCTTAAGATGCTAATAAGTTCATGTATTTGAGCAATTGAGAACATTTAAAGCAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAAAAG-ATTTGTTAATAATAA-------------------------------------------------------ATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCGTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAGTGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACACATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCCTGAAAAAACTGAAAAATCTGCAAAAAGGATGCATTAAATCTAAGAATTGTATTTCAGATAAAGTTGCAACATTTTTTGTTAATCATA----AAAAGTA-----------------------------------------TATATTTCTATCT--------AATGTGTGTATCTAATTAA-----------CAGCAATGACTAC-------------CTTT----------------AATTTTGATGTAGTTAT-TTTATATCTGTATATAAGCACATACACATATATATGACCTAGGTTTATTTATCAGTATTTTTATGCTGATAATAAGCATCACTGGAAATTAAT-----TTTCTTATGGAAATTATGTGGATCCAATGGATAAAATATGAGTTTATATAAATTAGTAAATGCCAAAATCAAGGAAGAAACAATTTTTATTTTAATTGTACTTTAAGTTAGATAAATGGTAAGGTCAACAGCTTGTTACAACCCTTAAGTATTATTTTCAGGCTGATTGTCAATATGTTTTGTACAatgttctcac +CTCTGCTTTGTGTGGAGAAG-TATTGTCC--------ACTCTGAATGATTTGGTAATA-------ATAATAATATATTTTGCTAATT--------------------------------ATATT---------------------------------------------------------------------------------------------TGTAA----TTTTTCTTATTTAACA-AGAAATGAGA-------ATTTTCTTATATTTCACTGATTTCTAacacacacacatatacacatcacatacacacaaagagagagacagagacacagagagacacagagagacagacagacagacagacagacagacagatacacagtcaCATTTCTCAATTCTCTATATCATT-GTTCACTT----TGCCTGATGGGTTTTTAGTAGCAATCATGTATATTTTAAT-CATTTTAATATTATAAAGATATCAGCTTTATTCTCTCTA-AACATTG-AAATTCAAGTACAAGATAAGCATGAGTTAGTTTTGTG---------ACAAGCATGTGTAAGAAATAATTCTTtctctctctctctctctctctctctctctctctctctctctctctccatttttctttctttctttTGGTACAGAGGATGAAAGTTCCACATGTGCTCTTAAAGCACTTTATCATTGAGTCTATTTTTTCAGTTGGCATAAGTAAAAATAAGTTAAGTGTTTTGACTCACCATTCTAATGCTTGATATTCACTTAATTTTATTAGTTTTAAATTTCAGTTTTAAAATAATTTTTTTAAGTTTTGAAAACAAT-----GTTAATGTCCTTACAGAGTCTTTTCATTTTCTGGACTACTGCATTCATTTAGGATTGTTCCCAATATCTCTTTTTATTTCACCTGCACTTGAGAATTTAATACATTTTATCCTACTACAT--AAATCGTGTCATGTTTATGT-TTTTATCAATTGCTATAATTTAATGCAGTATATCAT-TCTGAGTAGAGCTTTTTTCAAACTCCATAAATCTTATATACACTGGATTCCTCACATTTTGTAAATTGTCTAC-ACCAATTAAAAATACTTGTTAATAGAAATTGTTTTGATAAACAAATTGTCTAGTGTTAAACAATATCTCTGGTACAGTGACTGATTTTAAATGACTAACATTTAAT--CTTACTTT--GATGCCTTAAAATAATTCAT-CTTGTCTTTCAGGATTTTTATGTATTTTCCCAACTTTCTGATCCAATGGACCAAGTTAATGCTTCTGCTCTACCTGAATTTGTTTTGCTGGGACTTGCACAATCGTTTGGAACACAGATTTTCTTTGGCCTCTTCTTCTCCTTATTTTATGTGGGGATTCTTTTTGGAAACCTCTTCATTGTGTTCATAGTGATTGTTGATTCTCATTTACACTTCCCCATGTATATTCTATTGGCCAACCTTTCGCTCATTGACTTGGGCCTTTCATCTACAACAATTCCTAGGACAATATCTGATCTTTTTACTGGCTGTAAAGTCATTTCTTTCCACAGCTGCATGACACAAATGTTCTTCATTCATGTGATGGGTGGAGTTGAGATGGTACTGCTCATAGCCATGGCATATGACAGATATATAGCAATCTGCAAGCCTCTTCACTACCTGATGATCATGAATCCCAAAAAATGTATAATTTTGGTAATAGCAGCTTGGGTCATAGGGATGATTCATGCAGTGTCTCAGTTTCTGTTTGTTGTAAATTTACCCTTCTGTGGTCCCTACAATGTAGGAAGTTTTTATTGTGATTTTCCAAGGGTCATTAAACTTGCATGCATGGACACTTATAAACTAGAATTTGTGGTCTCTGCCAACAGTGGCTTTATTTCTATGTGTACCTTCTTTTTTCTGATTACATCATACATTTTTATCCTGGCCAGTGTACGACAACATTCTTCAACTGATTTATCCAAAGCATTTGTCACCTTGTCAGCTCACATCACTGTAGTGGTTTTGTTTTTCATACCATGCATGTTTCTGTATGTATGGCCATTTCCGACCAAGTCACTTGATAATTTCTTTGCTATTGTTGACTTTGTTCTCACTCCTGTCTTAAATCCTACTATCTATACTTTAAGGAATAAAGATATGAGGTTGGCCATCAGAAGGCTAAGTAGACAGGTTTTAAGTTCTAGGGAATTTATATAGTAAATTTTATTAGTATCAACACTGA--AAATGTGATAAACTATCAA---------------TATTAACACTATAGAATAAAAACATTATT-TTATTGGGTTTAGAAACATAAGAATGTAC--------------CTATCAAAGAGTTTCAATTAATAAGGAGTTACAATAACTTCTGCTGGTTACAAAATAAAAGTGTTATATGTTTTCAAATCAACATAACTAAATCTTGTTGGTTTTATATTTTTGTATTGAATTGAAGTATTCATATTTATTTAAGTTATTATAACCAGCAATTATTGCACAAATGTTCATGCTTTTTGGTTTGTATAAATAAATGTGCatatatatatatatatatatatatatatatatatatatatatatataAAATGAACC--TTTATCAGCATCTATATGCAGATAATA--CAACACTGGTTACTAATATATATTTCTTGTGGAAATTATGTGGATCCAATGGATAAA-----GGTTTATGTAAACCAATA------------------------------ATTTTAA------TTTAAGACTTATAAGTAGGA------------------------TAACCATCACTATTAAGAT-------------TTTTGTGTCCTTCTCTTAC diff --git a/tools/ucsc_tools/ucsc_axttomaf/test-data/hg38.noprefix.fasta.fai b/tools/ucsc_tools/ucsc_axttomaf/test-data/hg38.noprefix.fasta.fai new file mode 100644 index 00000000000..4c4cc48d41f --- /dev/null +++ b/tools/ucsc_tools/ucsc_axttomaf/test-data/hg38.noprefix.fasta.fai @@ -0,0 +1,24 @@ +chr1 248956422 11 50 51 +chr2 242193529 253935573 50 51 +chr3 198295559 500972984 50 51 +chr4 190214555 703234466 50 51 +chr5 181538259 897253324 50 51 +chr6 170805979 1082422360 50 51 +chr7 159345973 1256644470 50 51 +chr8 145138636 1419177374 50 51 +chr9 138394717 1567218794 50 51 +chr10 133797422 1708381418 50 51 +chr11 135086622 1844854801 50 51 +chr12 133275309 1982643168 50 51 +chr13 114364328 2118583996 50 51 +chr14 107043718 2235235623 50 51 +chr15 101991189 2344420228 50 51 +chr16 90338345 2448451253 50 51 +chr17 83257441 2540596377 50 51 +chr18 80373285 2625518979 50 51 +chr19 58617616 2707499742 50 51 +chr20 64444167 2767289723 50 51 +chr21 46709983 2833022786 50 51 +chr22 50818468 2880666981 50 51 +chrX 156040895 2932501830 50 51 +chrY 57227415 3091663554 50 51 diff --git a/tools/ucsc_tools/ucsc_axttomaf/test-data/mm39.noprefix.fasta.fai b/tools/ucsc_tools/ucsc_axttomaf/test-data/mm39.noprefix.fasta.fai new file mode 100644 index 00000000000..16f76b03e24 --- /dev/null +++ b/tools/ucsc_tools/ucsc_axttomaf/test-data/mm39.noprefix.fasta.fai @@ -0,0 +1,21 @@ +chr1 195154279 11 50 51 +chr10 130530862 199057388 50 51 +chr11 121973369 332198880 50 51 +chr12 120092757 456611729 50 51 +chr13 120883175 579106354 50 51 +chr14 125139656 702407205 50 51 +chr15 104073951 830049667 50 51 +chr16 98008968 936205110 50 51 +chr17 95294699 1036174270 50 51 +chr18 90720763 1133374875 50 51 +chr19 61420004 1225910066 50 51 +chr2 181755017 1288558482 50 51 +chr3 159745316 1473948611 50 51 +chr4 156860686 1636888845 50 51 +chr5 151758149 1796886756 50 51 +chr6 149588044 1951680079 50 51 +chr7 144995196 2104259895 50 51 +chr8 130127694 2252155006 50 51 +chr9 124359700 2384885265 50 51 +chrX 169476592 2511732170 50 51 +chrY 91455967 2684598305 50 51 From 7127d7a93456a3d0c1b6f16d9a11cfc5c5882ffa Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:25:29 +0000 Subject: [PATCH 23/36] Updating tools/humann from version 3.8 to 3.9 --- tools/humann/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/humann/macros.xml b/tools/humann/macros.xml index 97cc121b0d0..9d950a7c35e 100644 --- a/tools/humann/macros.xml +++ b/tools/humann/macros.xml @@ -1,6 +1,6 @@ - 3.8 + 3.9 0 22.01 From 7bbdea2cb04c430b60f4d7a92fda0ea6c20f4ee2 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:52:34 +0000 Subject: [PATCH 24/36] Updating tools/tsebra from version 1.1.2.4 to 1.1.2.5 --- tools/tsebra/macros.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/tsebra/macros.xml b/tools/tsebra/macros.xml index c0269b2d273..69602a39854 100644 --- a/tools/tsebra/macros.xml +++ b/tools/tsebra/macros.xml @@ -1,5 +1,5 @@ - 1.1.2.4 + 1.1.2.5 /10.1186/s12859-021-04482-0 From 7d29653a131bb160ee0bfa08fb7134eafcecfee8 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 26 Sep 2024 15:20:24 +0200 Subject: [PATCH 25/36] add profile --- tools/poretools/macros.xml | 1 + tools/poretools/poretools_events.xml | 2 +- tools/poretools/poretools_extract.xml | 2 +- tools/poretools/poretools_hist.xml | 2 +- tools/poretools/poretools_nucdist.xml | 2 +- tools/poretools/poretools_occupancy.xml | 2 +- tools/poretools/poretools_qualdist.xml | 2 +- tools/poretools/poretools_qualpos.xml | 2 +- tools/poretools/poretools_squiggle.xml | 2 +- tools/poretools/poretools_stats.xml | 2 +- tools/poretools/poretools_tabular.xml | 2 +- tools/poretools/poretools_times.xml | 2 +- tools/poretools/poretools_winner.xml | 2 +- tools/poretools/poretools_yield_plot.xml | 2 +- 14 files changed, 14 insertions(+), 13 deletions(-) diff --git a/tools/poretools/macros.xml b/tools/poretools/macros.xml index 3d901ebc11c..39aa8a86471 100644 --- a/tools/poretools/macros.xml +++ b/tools/poretools/macros.xml @@ -12,6 +12,7 @@ 0.6.1a1 + 23.1 10.1093/bioinformatics/btu555 diff --git a/tools/poretools/poretools_events.xml b/tools/poretools/poretools_events.xml index 0cd5969bf24..c8219d9fa4c 100644 --- a/tools/poretools/poretools_events.xml +++ b/tools/poretools/poretools_events.xml @@ -1,4 +1,4 @@ - + from a set of sequencing reads macros.xml diff --git a/tools/poretools/poretools_extract.xml b/tools/poretools/poretools_extract.xml index 6ca0c94c449..61c43aa7f6d 100644 --- a/tools/poretools/poretools_extract.xml +++ b/tools/poretools/poretools_extract.xml @@ -1,4 +1,4 @@ - + in FASTA or FASTQ format from nanopore files macros.xml diff --git a/tools/poretools/poretools_hist.xml b/tools/poretools/poretools_hist.xml index 8386e7063da..b65bb0c44ef 100644 --- a/tools/poretools/poretools_hist.xml +++ b/tools/poretools/poretools_hist.xml @@ -1,4 +1,4 @@ - + of nanopore read lengths macros.xml diff --git a/tools/poretools/poretools_nucdist.xml b/tools/poretools/poretools_nucdist.xml index 21924bf9e16..13d0b56c410 100644 --- a/tools/poretools/poretools_nucdist.xml +++ b/tools/poretools/poretools_nucdist.xml @@ -1,4 +1,4 @@ - + distribution in nanopore sequencing reads macros.xml diff --git a/tools/poretools/poretools_occupancy.xml b/tools/poretools/poretools_occupancy.xml index 3d25f1eb477..7bc14b5a213 100644 --- a/tools/poretools/poretools_occupancy.xml +++ b/tools/poretools/poretools_occupancy.xml @@ -1,4 +1,4 @@ - + per cell in nanopore reads macros.xml diff --git a/tools/poretools/poretools_qualdist.xml b/tools/poretools/poretools_qualdist.xml index ce313e17132..9fe1e5aef44 100644 --- a/tools/poretools/poretools_qualdist.xml +++ b/tools/poretools/poretools_qualdist.xml @@ -1,4 +1,4 @@ - + score distribution in nanopore sequencing reads macros.xml diff --git a/tools/poretools/poretools_qualpos.xml b/tools/poretools/poretools_qualpos.xml index c929f64a8dc..0d0a03f5610 100644 --- a/tools/poretools/poretools_qualpos.xml +++ b/tools/poretools/poretools_qualpos.xml @@ -1,4 +1,4 @@ - + plot of quality score distribution over positions in nanopore reads macros.xml diff --git a/tools/poretools/poretools_squiggle.xml b/tools/poretools/poretools_squiggle.xml index 576b451be65..38db80852cd 100644 --- a/tools/poretools/poretools_squiggle.xml +++ b/tools/poretools/poretools_squiggle.xml @@ -1,4 +1,4 @@ - + for nanopore reads macros.xml diff --git a/tools/poretools/poretools_stats.xml b/tools/poretools/poretools_stats.xml index a56371bb3b7..14dc24a7253 100644 --- a/tools/poretools/poretools_stats.xml +++ b/tools/poretools/poretools_stats.xml @@ -1,4 +1,4 @@ - + from a set of FAST5 files macros.xml diff --git a/tools/poretools/poretools_tabular.xml b/tools/poretools/poretools_tabular.xml index 912147fecf7..b3f4ecae0ea 100644 --- a/tools/poretools/poretools_tabular.xml +++ b/tools/poretools/poretools_tabular.xml @@ -1,4 +1,4 @@ - + in tabular format from a set of FAST5 files macros.xml diff --git a/tools/poretools/poretools_times.xml b/tools/poretools/poretools_times.xml index 7522d695467..5490cdc160e 100644 --- a/tools/poretools/poretools_times.xml +++ b/tools/poretools/poretools_times.xml @@ -1,4 +1,4 @@ - + and channel information from a set of FAST5 files macros.xml diff --git a/tools/poretools/poretools_winner.xml b/tools/poretools/poretools_winner.xml index c27ba4c95bd..9802e7cb7b1 100644 --- a/tools/poretools/poretools_winner.xml +++ b/tools/poretools/poretools_winner.xml @@ -1,4 +1,4 @@ - + from a set of FAST5 files. macros.xml diff --git a/tools/poretools/poretools_yield_plot.xml b/tools/poretools/poretools_yield_plot.xml index ca516f11ec5..0034f370511 100644 --- a/tools/poretools/poretools_yield_plot.xml +++ b/tools/poretools/poretools_yield_plot.xml @@ -1,4 +1,4 @@ - + of sequencing yield over time macros.xml From a4e266b49ca33d08b886a52dc0845dc33a4a608b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Thu, 26 Sep 2024 16:24:10 +0200 Subject: [PATCH 26/36] Remove wrappers of removed commands --- tools/humann/humann_associate.xml | 77 ---------------- tools/humann/humann_rna_dna_norm.xml | 117 ------------------------ tools/humann/humann_strain_profiler.xml | 68 -------------- 3 files changed, 262 deletions(-) delete mode 100644 tools/humann/humann_associate.xml delete mode 100644 tools/humann/humann_rna_dna_norm.xml delete mode 100644 tools/humann/humann_strain_profiler.xml diff --git a/tools/humann/humann_associate.xml b/tools/humann/humann_associate.xml deleted file mode 100644 index 5cfa4ba2de5..00000000000 --- a/tools/humann/humann_associate.xml +++ /dev/null @@ -1,77 +0,0 @@ - - on HUMAnN generated table - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tools/humann/humann_rna_dna_norm.xml b/tools/humann/humann_rna_dna_norm.xml deleted file mode 100644 index 624489dae23..00000000000 --- a/tools/humann/humann_rna_dna_norm.xml +++ /dev/null @@ -1,117 +0,0 @@ - - combined meta'omic sequencing data - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/tools/humann/humann_strain_profiler.xml b/tools/humann/humann_strain_profiler.xml deleted file mode 100644 index f9a07a461f3..00000000000 --- a/tools/humann/humann_strain_profiler.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - From c2e1750134a51454bb6603aa47797a2cc8b1ca3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 26 Sep 2024 17:21:12 +0200 Subject: [PATCH 27/36] Update poretools_squiggle.xml --- tools/poretools/poretools_squiggle.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/poretools/poretools_squiggle.xml b/tools/poretools/poretools_squiggle.xml index 38db80852cd..3d9e56d8cf4 100644 --- a/tools/poretools/poretools_squiggle.xml +++ b/tools/poretools/poretools_squiggle.xml @@ -1,4 +1,4 @@ - + for nanopore reads macros.xml From 567c48b703911b51ff6870d9eba20bc9aea1367c Mon Sep 17 00:00:00 2001 From: M Bernt Date: Fri, 27 Sep 2024 09:00:30 +0200 Subject: [PATCH 28/36] Update tools/poretools/macros.xml --- tools/poretools/macros.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/tools/poretools/macros.xml b/tools/poretools/macros.xml index 39aa8a86471..a53e3ca49fc 100644 --- a/tools/poretools/macros.xml +++ b/tools/poretools/macros.xml @@ -54,5 +54,4 @@ - 18.09 From c20a8bd3354f424b08b665e2022f9a99c76eddc9 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 27 Sep 2024 10:11:26 +0200 Subject: [PATCH 29/36] Update falco to v1.2.4 --- tools/falco/falco.xml | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/tools/falco/falco.xml b/tools/falco/falco.xml index 7d12090a805..aae928e08cb 100644 --- a/tools/falco/falco.xml +++ b/tools/falco/falco.xml @@ -1,7 +1,7 @@ An alternative, more performant implementation of FastQC for high throughput sequence quality control - 1.2.3 + 1.2.4 0 @@ -159,15 +159,15 @@ Falco_ is a high-speed emulation of the popular FastQC software for quality cont 💚️ With its superior performance Falco saves computational resources and gives you back results faster than FastQC. -We recommend it for most use cases (but see below for exceptions). 💚️ +We recommend it for most use cases (but see below for rare exceptions). 💚️ The main functions of Falco are very similar to those of FastQC: - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data -- Export of results to an HTML based permanent report -- Offline operation to allow automated generation of reports without running the interactive application +- Export of results to an HTML-based report + .. class:: infomark @@ -181,13 +181,10 @@ The plain text report generated by Falco can be used as a "FastQC" report in Mul Falco doesn't currently support fastq.bz2 as input format meaning Galaxy has to perform a relatively slow format conversion before running the tool, which together makes the analysis slower than with FastQC. -- you are interested in PolyA and PolyG statistics in the Adapter Content section of the quality report - - Falco doesn't currently calculate statistics for these "Adapters" by default. - -- your input consists of *mapped* reads in SAM/BAM format +- you need the HTML report to be viewable offline - Due to a bug in the current version of Falco, reads mapped to the reverse strand of the reference genome are not handled correctly and reported metrics are wrong! + The current version of Falco relies on plotly to generate the graphs in the HTML report dynamically each time it's viewed. + MultiQC plots generated from Falco's raw data output are, of course, viewable offline just like the ones generated from FastQC output. ----- From a181178679b957b9ea1c4d30e7051ab49bec2e8f Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 27 Sep 2024 12:26:35 +0200 Subject: [PATCH 30/36] Improve tests and update test-data - part 1 --- tools/falco/falco.xml | 64 +- tools/falco/test-data/contaminant_list.txt | 386 ++-- tools/falco/test-data/fastqc_data.txt | 218 +-- .../falco/test-data/fastqc_data_adapters.txt | 72 +- .../test-data/fastqc_data_contaminants.txt | 2 +- .../test-data/fastqc_data_customlimits.txt | 1636 +---------------- tools/falco/test-data/limits.txt | 162 +- 7 files changed, 470 insertions(+), 2070 deletions(-) diff --git a/tools/falco/falco.xml b/tools/falco/falco.xml index aae928e08cb..5fb9d98b30c 100644 --- a/tools/falco/falco.xml +++ b/tools/falco/falco.xml @@ -76,26 +76,42 @@ - - + + + + + + - - + + + + + + - - + + + + + + - - + + + + + + @@ -83,6 +84,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -103,7 +136,7 @@ - + @@ -111,7 +144,8 @@ - + + - + - - - - - @@ -171,17 +200,15 @@ - + - - tm1`~^I_S&Qz!xeYbl zfZe-XXV2R?6Nxmlv;dV1{%l&HB$R20bhQek6a)a2LWpBkAa_FE0So{D+EOwA06?Td z5;H=i0sxTT3jaUQqF$+?5Jnk@)*9voOBEFW7vNSG0stA@Mq_DZ?04Kp)S|83qvPOn zx`1)?;+gqsea;tv3iTOF#O5zHjP_z28y-}-afB^}> zo5dG0Sod>bQN-lCiyH;PEslW!Q3c)*Cwv4DTwMVGIuhS^0C^(Sd(9Ax!4aAvjUJL^ zJsDH4*!jP9set;HR9Iv2C>Wz^I*=EDWhgZ|oj0xoxKcx=+5e-%Lt>dKReOXY@WeqP z6A@ZQND3ahESl}L4U=rK{~Ce+Cnkzy-M46$L-4}lz)&7aN(SoXtuz3EwC+S}&Gx@) z0Kk70RTyMB(lFo*0wo9mNh9JR;sL-S`2a+4w_saWGT{HI{*MqvM*?meaclh~I%<0v zKx8QnfG)oSP-sMof5ZV8Ro>yXL+$`j3gm!V*M}9%o?-Fd%~ig!>}@QyByk3;+O;xnjtdnN)yy90M^nTUWZV%>h%L z!R|g}EaR4eV8+!BXi6>$*|qe&2siIa6|LFvTkB+S)q%|1=jBATX6)_4|N0n-c3Xqax>nujC< ziBY{LD>z9b(h-6;T8wJ+a!+=%7$Yu^ctc5UA&`$kd79&4vFe*KL8wH?x5d?L3glG- z(Gtl4;DCm}V*pS9-FC#CAR?5kN|h$py4s;ptx;KHMkS%vC=LxGPS-@$qSUIu3@8Hv 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-quality_base ignore 0 -sequence ignore 0 -gc_sequence ignore 0 -quality_sequence ignore 0 -tile ignore 0 -sequence_length ignore 0 -adapter ignore 0 - -# For the duplication module the value is the percentage -# remaining after deduplication. Measured levels below -# these limits trigger the warning / error. -duplication warn 70 -duplication error 50 - -# For the kmer module the filter is on the -log10 binomial -# pvalue for the most significant Kmer, so 5 would be -# 10^-5 = p<0.00001 -kmer warn 2 -kmer error 5 - -# For the N module the filter is on the percentage of Ns -# at any position in the library -n_content warn 5 -n_content error 20 - -# For the overrepresented seqs the warn value sets the -# threshold for the overrepresented sequences to be reported -# at all as the proportion of the library which must be seen -# as a single sequence -overrepresented warn 0.1 -overrepresented error 1 - -# The per base quality filter uses two values, one for the value -# of the lower quartile, and the other for the value of the -# median quality. Failing either of these will trigger the alert -quality_base_lower warn 10 -quality_base_lower error 5 -quality_base_median warn 25 -quality_base_median error 20 - -# The per base sequence content module tests the maximum deviation -# between A and T or C and G -sequence warn 10 -sequence error 20 - -# The per sequence GC content tests the maximum deviation between -# the theoretical distribution and the real distribution -gc_sequence warn 15 -gc_sequence error 30 - -# The per sequence quality module tests the phred score which is -# most frequently observed -quality_sequence warn 27 -quality_sequence error 20 - -# The per tile module tests the maximum phred score loss between -# and individual tile and the average for that base across all tiles -tile warn 5 -tile error 10 - -# The sequence length module tests are binary, so the values here -# simply turn them on or off. The actual tests warn if you have -# sequences of different length, and error if you have sequences -# of zero length. - -sequence_length warn 1 -sequence_length error 1 - -# The adapter module's warnings and errors are based on the -# percentage of reads in the library which have been observed -# to contain an adapter associated Kmer at any point - -adapter warn 5 -adapter error 10 - - - diff --git a/tools/falco/test-data/fastqc_data_contaminant_summary.txt b/tools/falco/test-data/fastqc_data_contaminant_summary.txt deleted file mode 100644 index 109484ffc6f..00000000000 --- a/tools/falco/test-data/fastqc_data_contaminant_summary.txt +++ /dev/null @@ -1,11 +0,0 @@ -PASS Basic Statistics 1000trimmed_fastq -PASS Per base sequence quality 1000trimmed_fastq -FAIL Per tile sequence quality 1000trimmed_fastq -PASS Per sequence quality scores 1000trimmed_fastq -FAIL Per base sequence content 1000trimmed_fastq -WARN Per sequence GC content 1000trimmed_fastq -PASS Per base N content 1000trimmed_fastq -WARN Sequence Length Distribution 1000trimmed_fastq -PASS Sequence Duplication Levels 1000trimmed_fastq -WARN Overrepresented sequences 1000trimmed_fastq -PASS Adapter Content 1000trimmed_fastq diff --git a/tools/falco/test-data/fastqc_data_contaminants.txt b/tools/falco/test-data/fastqc_data_contaminants.txt index 6b8283d09e5..5218d3e1cdf 100644 --- a/tools/falco/test-data/fastqc_data_contaminants.txt +++ b/tools/falco/test-data/fastqc_data_contaminants.txt @@ -1,4 +1,4 @@ -##Falco 1.2.3 +##Falco 1.2.4 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq @@ -1597,114 +1597,114 @@ Sequence length 1-108 #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672783 Test sequence >>END_MODULE ->>Adapter Content warn +>>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG 1 0 0 0 0 0.0203874 0 -2 0 0 0 0 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0.468909 0 0 0 0.326198 0 +108 0.468909 0 0 0 0.326198 0 >>END_MODULE diff --git a/tools/falco/test-data/fastqc_data_customlimits.txt b/tools/falco/test-data/fastqc_data_customlimits.txt deleted file mode 100644 index 6730a97717f..00000000000 --- a/tools/falco/test-data/fastqc_data_customlimits.txt +++ /dev/null @@ -1,76 +0,0 @@ -##Falco 1.2.4 ->>Basic Statistics pass -#Measure Value -Filename 1000trimmed_fastq -File type Conventional base calls -Encoding Sanger / Illumina 1.9 -Total Sequences 4905 -Sequences flagged as poor quality 0 -Sequence length 1-108 -%GC 41 ->>END_MODULE ->>Sequence Length Distribution warn -#Length Count -1 3.0 -2 11.0 -3 28.0 -4 56.0 -5 43.0 -6 52.0 -7 39.0 -8 56.0 -9 60.0 -10 57.0 -11 43.0 -12 46.0 -13 45.0 -14 66.0 -15 59.0 -16 49.0 -17 73.0 -18 54.0 -19 44.0 -20 52.0 -21 73.0 -22 72.0 -23 68.0 -24 56.0 -25 86.0 -26 92.0 -27 75.0 -28 69.0 -29 74.0 -30 96.0 -31 72.0 -32 81.0 -33 65.0 -34 87.0 -35 86.0 -36 87.0 -37 100.0 -38 82.0 -39 78.0 -40 76.0 -41 79.0 -42 88.0 -43 83.0 -44 75.0 -45 74.0 -46 72.0 -47 84.0 -48 74.0 -49 81.0 -50 91.0 -51 80.0 -52 98.0 -53 43.0 -54 8.0 -55 4.0 -56 1.0 -64 1.0 -97 1.0 -98 32.0 -106 34.0 -107 169.0 -108 1122.0 ->>END_MODULE diff --git a/tools/falco/test-data/fastqc_data_customlimits_summary.txt b/tools/falco/test-data/fastqc_data_customlimits_summary.txt index 109484ffc6f..1d639fa65f6 100644 --- a/tools/falco/test-data/fastqc_data_customlimits_summary.txt +++ b/tools/falco/test-data/fastqc_data_customlimits_summary.txt @@ -1,11 +1,2 @@ PASS Basic Statistics 1000trimmed_fastq -PASS Per base sequence quality 1000trimmed_fastq -FAIL Per tile sequence quality 1000trimmed_fastq -PASS Per sequence quality scores 1000trimmed_fastq -FAIL Per base sequence content 1000trimmed_fastq -WARN Per sequence GC content 1000trimmed_fastq -PASS Per base N content 1000trimmed_fastq WARN Sequence Length Distribution 1000trimmed_fastq -PASS Sequence Duplication Levels 1000trimmed_fastq -WARN Overrepresented sequences 1000trimmed_fastq -PASS Adapter Content 1000trimmed_fastq diff --git a/tools/falco/test-data/fastqc_data_hisat.txt b/tools/falco/test-data/fastqc_data_hisat.txt index fda438ce067..96e52740c79 100644 --- a/tools/falco/test-data/fastqc_data_hisat.txt +++ b/tools/falco/test-data/fastqc_data_hisat.txt @@ -1,448 +1,601 @@ -##FastQC 0.12.1 +##Falco 1.2.4 >>Basic Statistics pass #Measure Value Filename hisat_output_1_bam File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 20 -Total Bases 1.4 kbp Sequences flagged as poor quality 0 Sequence length 70 -%GC 43 +%GC 44 >>END_MODULE ->>Per base sequence quality pass +>>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile -1 17.0 NaN NaN NaN NaN NaN -2 17.0 NaN NaN NaN NaN NaN -3 17.0 NaN NaN NaN NaN NaN -4 17.0 NaN NaN NaN NaN NaN -5 17.0 NaN NaN NaN NaN NaN -6 17.0 NaN NaN NaN NaN NaN -7 17.0 NaN NaN NaN NaN NaN -8 17.0 NaN NaN NaN NaN NaN -9 17.0 NaN NaN NaN NaN NaN -10 17.0 NaN NaN NaN NaN NaN -11 17.0 NaN NaN NaN NaN NaN -12 17.0 NaN NaN NaN NaN NaN -13 17.0 NaN NaN NaN NaN NaN -14 17.0 NaN NaN NaN NaN NaN -15 17.0 NaN NaN NaN NaN NaN -16 17.0 NaN NaN NaN NaN NaN -17 17.0 NaN NaN NaN NaN NaN -18 17.0 NaN NaN NaN NaN NaN -19 17.0 NaN NaN NaN NaN NaN -20 17.0 NaN NaN NaN NaN NaN -21 17.0 NaN NaN NaN NaN NaN -22 17.0 NaN NaN NaN NaN NaN -23 17.0 NaN NaN NaN NaN NaN -24 17.0 NaN NaN NaN NaN NaN -25 17.0 NaN NaN NaN NaN NaN -26 17.0 NaN NaN NaN NaN NaN -27 17.0 NaN NaN NaN NaN NaN -28 17.0 NaN NaN NaN NaN NaN -29 17.0 NaN NaN NaN NaN NaN -30 17.0 NaN NaN NaN NaN NaN -31 17.0 NaN NaN NaN NaN NaN -32 17.0 NaN NaN NaN NaN NaN -33 17.0 NaN NaN NaN NaN NaN -34 17.0 NaN NaN NaN NaN NaN -35 17.0 NaN NaN NaN NaN NaN -36 17.0 NaN NaN NaN NaN NaN -37 17.0 NaN NaN NaN NaN NaN -38 17.0 NaN NaN NaN NaN NaN -39 17.0 NaN NaN NaN NaN NaN -40 17.0 NaN NaN NaN NaN NaN -41 17.0 NaN NaN NaN NaN NaN -42 17.0 NaN NaN NaN NaN NaN -43 17.0 NaN NaN NaN NaN NaN -44 17.0 NaN NaN NaN NaN NaN -45 17.0 NaN NaN NaN NaN NaN -46 17.0 NaN NaN NaN NaN NaN -47 17.0 NaN NaN NaN NaN NaN -48 17.0 NaN NaN NaN NaN NaN -49 17.0 NaN NaN NaN NaN NaN -50 17.0 NaN NaN NaN NaN NaN -51 17.0 NaN NaN NaN NaN NaN -52 17.0 NaN NaN NaN NaN NaN -53 17.0 NaN NaN NaN NaN NaN -54 17.0 NaN NaN NaN NaN NaN -55 17.0 NaN NaN NaN NaN NaN -56 17.0 NaN NaN NaN NaN NaN -57 17.0 NaN NaN NaN NaN NaN -58 17.0 NaN NaN NaN NaN NaN -59 17.0 NaN NaN NaN NaN NaN -60 17.0 NaN NaN NaN NaN NaN -61 17.0 NaN NaN NaN NaN NaN -62 17.0 NaN NaN NaN NaN NaN -63 17.0 NaN NaN NaN NaN NaN -64 17.0 NaN NaN NaN NaN NaN -65 17.0 NaN NaN NaN NaN NaN -66 17.0 NaN NaN NaN NaN NaN -67 17.0 NaN NaN NaN NaN NaN -68 17.0 NaN NaN NaN NaN NaN -69 17.0 NaN NaN NaN NaN NaN -70 17.0 NaN NaN NaN NaN NaN +1 17 17 17 17 17 17 +2 17 17 17 17 17 17 +3 17 17 17 17 17 17 +4 17 17 17 17 17 17 +5 17 17 17 17 17 17 +6 17 17 17 17 17 17 +7 17 17 17 17 17 17 +8 17 17 17 17 17 17 +9 17 17 17 17 17 17 +10 17 17 17 17 17 17 +11 17 17 17 17 17 17 +12 17 17 17 17 17 17 +13 17 17 17 17 17 17 +14 17 17 17 17 17 17 +15 17 17 17 17 17 17 +16 17 17 17 17 17 17 +17 17 17 17 17 17 17 +18 17 17 17 17 17 17 +19 17 17 17 17 17 17 +20 17 17 17 17 17 17 +21 17 17 17 17 17 17 +22 17 17 17 17 17 17 +23 17 17 17 17 17 17 +24 17 17 17 17 17 17 +25 17 17 17 17 17 17 +26 17 17 17 17 17 17 +27 17 17 17 17 17 17 +28 17 17 17 17 17 17 +29 17 17 17 17 17 17 +30 17 17 17 17 17 17 +31 17 17 17 17 17 17 +32 17 17 17 17 17 17 +33 17 17 17 17 17 17 +34 17 17 17 17 17 17 +35 17 17 17 17 17 17 +36 17 17 17 17 17 17 +37 17 17 17 17 17 17 +38 17 17 17 17 17 17 +39 17 17 17 17 17 17 +40 17 17 17 17 17 17 +41 17 17 17 17 17 17 +42 17 17 17 17 17 17 +43 17 17 17 17 17 17 +44 17 17 17 17 17 17 +45 17 17 17 17 17 17 +46 17 17 17 17 17 17 +47 17 17 17 17 17 17 +48 17 17 17 17 17 17 +49 17 17 17 17 17 17 +50 17 17 17 17 17 17 +51 17 17 17 17 17 17 +52 17 17 17 17 17 17 +53 17 17 17 17 17 17 +54 17 17 17 17 17 17 +55 17 17 17 17 17 17 +56 17 17 17 17 17 17 +57 17 17 17 17 17 17 +58 17 17 17 17 17 17 +59 17 17 17 17 17 17 +60 17 17 17 17 17 17 +61 17 17 17 17 17 17 +62 17 17 17 17 17 17 +63 17 17 17 17 17 17 +64 17 17 17 17 17 17 +65 17 17 17 17 17 17 +66 17 17 17 17 17 17 +67 17 17 17 17 17 17 +68 17 17 17 17 17 17 +69 17 17 17 17 17 17 +70 17 17 17 17 17 17 +>>END_MODULE +>>Per tile sequence quality pass +#Tile Base Mean +470 1 0 +470 2 0 +470 3 0 +470 4 0 +470 5 0 +470 6 0 +470 7 0 +470 8 0 +470 9 0 +470 10 0 +470 11 0 +470 12 0 +470 13 0 +470 14 0 +470 15 0 +470 16 0 +470 17 0 +470 18 0 +470 19 0 +470 20 0 +470 21 0 +470 22 0 +470 23 0 +470 24 0 +470 25 0 +470 26 0 +470 27 0 +470 28 0 +470 29 0 +470 30 0 +470 31 0 +470 32 0 +470 33 0 +470 34 0 +470 35 0 +470 36 0 +470 37 0 +470 38 0 +470 39 0 +470 40 0 +470 41 0 +470 42 0 +470 43 0 +470 44 0 +470 45 0 +470 46 0 +470 47 0 +470 48 0 +470 49 0 +470 50 0 +470 51 0 +470 52 0 +470 53 0 +470 54 0 +470 55 0 +470 56 0 +470 57 0 +470 58 0 +470 59 0 +470 60 0 +470 61 0 +470 62 0 +470 63 0 +470 64 0 +470 65 0 +470 66 0 +470 67 0 +470 68 0 +470 69 0 +470 70 0 +473 1 0 +473 2 0 +473 3 0 +473 4 0 +473 5 0 +473 6 0 +473 7 0 +473 8 0 +473 9 0 +473 10 0 +473 11 0 +473 12 0 +473 13 0 +473 14 0 +473 15 0 +473 16 0 +473 17 0 +473 18 0 +473 19 0 +473 20 0 +473 21 0 +473 22 0 +473 23 0 +473 24 0 +473 25 0 +473 26 0 +473 27 0 +473 28 0 +473 29 0 +473 30 0 +473 31 0 +473 32 0 +473 33 0 +473 34 0 +473 35 0 +473 36 0 +473 37 0 +473 38 0 +473 39 0 +473 40 0 +473 41 0 +473 42 0 +473 43 0 +473 44 0 +473 45 0 +473 46 0 +473 47 0 +473 48 0 +473 49 0 +473 50 0 +473 51 0 +473 52 0 +473 53 0 +473 54 0 +473 55 0 +473 56 0 +473 57 0 +473 58 0 +473 59 0 +473 60 0 +473 61 0 +473 62 0 +473 63 0 +473 64 0 +473 65 0 +473 66 0 +473 67 0 +473 68 0 +473 69 0 +473 70 0 >>END_MODULE >>Per sequence quality scores fail #Quality Count -17 20.0 +17 20 >>END_MODULE >>Per base sequence content fail #Base G A T C -1 20.0 5.0 35.0 40.0 -2 10.0 10.0 45.0 35.0 -3 35.0 20.0 20.0 25.0 -4 35.0 30.0 25.0 10.0 -5 20.0 20.0 30.0 30.0 -6 20.0 35.0 20.0 25.0 -7 15.0 40.0 35.0 10.0 -8 20.0 15.0 45.0 20.0 -9 20.0 25.0 35.0 20.0 -10 20.0 20.0 30.0 30.0 -11 15.0 20.0 45.0 20.0 -12 10.0 40.0 35.0 15.0 -13 25.0 35.0 20.0 20.0 -14 35.0 20.0 20.0 25.0 -15 30.0 35.0 15.0 20.0 -16 10.0 45.0 25.0 20.0 -17 25.0 25.0 40.0 10.0 -18 25.0 35.0 10.0 30.0 -19 5.0 30.0 25.0 40.0 -20 20.0 15.0 40.0 25.0 -21 25.0 25.0 25.0 25.0 -22 15.0 30.0 20.0 35.0 -23 20.0 5.0 45.0 30.0 -24 10.0 30.0 35.0 25.0 -25 30.0 40.0 15.0 15.0 -26 15.0 35.0 20.0 30.0 -27 15.0 35.0 30.0 20.0 -28 25.0 25.0 30.0 20.0 -29 15.0 30.0 20.0 35.0 -30 20.0 35.0 30.0 15.0 -31 20.0 35.0 25.0 20.0 -32 35.0 15.0 35.0 15.0 -33 30.0 35.0 15.0 20.0 -34 25.0 25.0 25.0 25.0 -35 25.0 20.0 35.0 20.0 -36 30.0 25.0 20.0 25.0 -37 15.0 45.0 25.0 15.0 -38 30.0 25.0 35.0 10.0 -39 20.0 45.0 15.0 20.0 -40 15.0 35.0 20.0 30.0 -41 35.0 25.0 20.0 20.0 -42 30.0 30.0 35.0 5.0 -43 25.0 15.0 40.0 20.0 -44 40.0 20.0 30.0 10.0 -45 15.0 35.0 25.0 25.0 -46 15.0 30.0 40.0 15.0 -47 35.0 15.0 30.0 20.0 -48 30.0 35.0 20.0 15.0 -49 10.0 55.00000000000001 30.0 5.0 -50 40.0 25.0 20.0 15.0 -51 25.0 35.0 10.0 30.0 -52 30.0 25.0 20.0 25.0 -53 30.0 10.0 30.0 30.0 -54 20.0 40.0 20.0 20.0 -55 10.0 35.0 10.0 45.0 -56 50.0 10.0 30.0 10.0 -57 15.0 45.0 30.0 10.0 -58 20.0 35.0 20.0 25.0 -59 30.0 35.0 30.0 5.0 -60 20.0 35.0 25.0 20.0 -61 25.0 15.0 35.0 25.0 -62 10.0 20.0 55.00000000000001 15.0 -63 25.0 20.0 35.0 20.0 -64 20.0 35.0 25.0 20.0 -65 30.0 35.0 25.0 10.0 -66 15.0 40.0 35.0 10.0 -67 20.0 35.0 20.0 25.0 -68 20.0 25.0 30.0 25.0 -69 15.0 35.0 25.0 25.0 -70 5.0 40.0 40.0 15.0 +1 20 5 35 40 +2 10 10 45 35 +3 35 20 20 25 +4 35 30 25 10 +5 20 20 30 30 +6 20 35 20 25 +7 15 40 35 10 +8 20 15 45 20 +9 20 25 35 20 +10 20 20 30 30 +11 15 20 45 20 +12 10 40 35 15 +13 25 35 20 20 +14 35 20 20 25 +15 30 35 15 20 +16 10 45 25 20 +17 25 25 40 10 +18 25 35 10 30 +19 5 30 25 40 +20 20 15 40 25 +21 25 25 25 25 +22 15 30 20 35 +23 20 5 45 30 +24 10 30 35 25 +25 30 40 15 15 +26 15 35 20 30 +27 15 35 30 20 +28 25 25 30 20 +29 15 30 20 35 +30 20 35 30 15 +31 20 35 25 20 +32 35 15 35 15 +33 30 35 15 20 +34 25 25 25 25 +35 25 20 35 20 +36 30 25 20 25 +37 15 45 25 15 +38 30 25 35 10 +39 20 45 15 20 +40 15 35 20 30 +41 35 25 20 20 +42 30 30 35 5 +43 25 15 40 20 +44 40 20 30 10 +45 15 35 25 25 +46 15 30 40 15 +47 35 15 30 20 +48 30 35 20 15 +49 10 55 30 5 +50 40 25 20 15 +51 25 35 10 30 +52 30 25 20 25 +53 30 10 30 30 +54 20 40 20 20 +55 10 35 10 45 +56 50 10 30 10 +57 15 45 30 10 +58 20 35 20 25 +59 30 35 30 5 +60 20 35 25 20 +61 25 15 35 25 +62 10 20 55 15 +63 25 20 35 20 +64 20 35 25 20 +65 30 35 25 10 +66 15 40 35 10 +67 20 35 20 25 +68 20 25 30 25 +69 15 35 25 25 +70 5 40 40 15 >>END_MODULE >>Per sequence GC content fail #GC Content Count -0 0.0 -1 0.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 -10 0.0 -11 0.0 -12 0.0 -13 0.0 -14 0.0 -15 0.0 -16 0.0 -17 0.0 -18 0.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.0 -27 0.0 -28 0.0 +0 0 +1 0 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 0 +10 0 +11 0 +12 0 +13 0 +14 0 +15 0 +16 0 +17 0 +18 0 +19 0 +20 0 +21 0 +22 0 +23 0 +24 0 +25 0 +26 0 +27 0 +28 0 29 0.5 -30 1.0 +30 1 31 0.5 32 0.5 -33 1.0 +33 1 34 0.5 -35 0.0 -36 0.0 -37 0.0 -38 1.0 +35 0 +36 0 +37 0 +38 1 39 2.5 -40 3.0 -41 2.0 +40 3 +41 2 42 1.5 -43 2.0 +43 2 44 2.5 45 2.5 -46 1.0 -47 0.0 +46 1 +47 0 48 0.5 49 0.5 -50 0.0 +50 0 51 1.5 52 1.5 -53 0.0 +53 0 54 0.5 55 0.5 -56 0.0 -57 0.0 -58 0.0 -59 0.0 -60 0.0 -61 0.0 -62 0.0 -63 0.0 -64 0.0 -65 0.0 -66 0.0 -67 0.0 -68 0.0 -69 0.0 -70 0.0 -71 0.0 -72 0.0 -73 0.0 -74 0.0 -75 0.0 -76 0.0 -77 0.0 -78 0.0 -79 0.0 -80 0.0 -81 0.0 -82 0.0 -83 0.0 -84 0.0 -85 0.0 -86 0.0 -87 0.0 -88 0.0 -89 0.0 -90 0.0 -91 0.0 -92 0.0 -93 0.0 -94 0.0 -95 0.0 -96 0.0 -97 0.0 -98 0.0 -99 0.0 -100 0.0 +56 0 +57 0 +58 0 +59 0 +60 0 +61 0 +62 0 +63 0 +64 0 +65 0 +66 0 +67 0 +68 0 +69 0 +70 0 +71 0 +72 0 +73 0 +74 0 +75 0 +76 0 +77 0 +78 0 +79 0 +80 0 +81 0 +82 0 +83 0 +84 0 +85 0 +86 0 +87 0 +88 0 +89 0 +90 0 +91 0 +92 0 +93 0 +94 0 +95 0 +96 0 +97 0 +98 0 +99 0 +100 0 >>END_MODULE >>Per base N content pass #Base N-Count -1 0.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 -10 0.0 -11 0.0 -12 0.0 -13 0.0 -14 0.0 -15 0.0 -16 0.0 -17 0.0 -18 0.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.0 -27 0.0 -28 0.0 -29 0.0 -30 0.0 -31 0.0 -32 0.0 -33 0.0 -34 0.0 -35 0.0 -36 0.0 -37 0.0 -38 0.0 -39 0.0 -40 0.0 -41 0.0 -42 0.0 -43 0.0 -44 0.0 -45 0.0 -46 0.0 -47 0.0 -48 0.0 -49 0.0 -50 0.0 -51 0.0 -52 0.0 -53 0.0 -54 0.0 -55 0.0 -56 0.0 -57 0.0 -58 0.0 -59 0.0 -60 0.0 -61 0.0 -62 0.0 -63 0.0 -64 0.0 -65 0.0 -66 0.0 -67 0.0 -68 0.0 -69 0.0 -70 0.0 +1 0 +2 0 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 0 +10 0 +11 0 +12 0 +13 0 +14 0 +15 0 +16 0 +17 0 +18 0 +19 0 +20 0 +21 0 +22 0 +23 0 +24 0 +25 0 +26 0 +27 0 +28 0 +29 0 +30 0 +31 0 +32 0 +33 0 +34 0 +35 0 +36 0 +37 0 +38 0 +39 0 +40 0 +41 0 +42 0 +43 0 +44 0 +45 0 +46 0 +47 0 +48 0 +49 0 +50 0 +51 0 +52 0 +53 0 +54 0 +55 0 +56 0 +57 0 +58 0 +59 0 +60 0 +61 0 +62 0 +63 0 +64 0 +65 0 +66 0 +67 0 +68 0 +69 0 +70 0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 70 20.0 >>END_MODULE >>Sequence Duplication Levels pass -#Total Deduplicated Percentage 100.0 -#Duplication Level Percentage of total -1 100.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 ->10 0.0 ->50 0.0 ->100 0.0 ->500 0.0 ->1k 0.0 ->5k 0.0 ->10k+ 0.0 +#Total Deduplicated Percentage 100 +#Duplication Level Percentage of deduplicated Percentage of total +1 100 100 +2 0 0 +3 0 0 +4 0 0 +5 0 0 +6 0 0 +7 0 0 +8 0 0 +9 0 0 +>10 0 0 +>50 0 0 +>100 0 0 +>500 0 0 +>1k 0 0 +>5k 0 0 +>10k+ 0 0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source -CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAG 1 5.0 No Hit -TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTA 1 5.0 No Hit -ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAG 1 5.0 No Hit -TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATG 1 5.0 No Hit -CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT 1 5.0 No Hit -TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTC 1 5.0 No Hit -CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTT 1 5.0 No Hit -TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAG 1 5.0 No Hit -CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAG 1 5.0 No Hit -GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAG 1 5.0 No Hit -CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTAT 1 5.0 No Hit -GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAA 1 5.0 No Hit -GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAG 1 5.0 No Hit -CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCAC 1 5.0 No Hit -TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACC 1 5.0 No Hit -CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATA 1 5.0 No Hit -TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAG 1 5.0 No Hit -GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGA 1 5.0 No Hit -TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATT 1 5.0 No Hit -CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAA 1 5.0 No Hit +ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC 1 5 No Hit +GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA 1 5 No Hit +CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT 1 5 No Hit +CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA 1 5 No Hit +CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA 1 5 No Hit +CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT 1 5 No Hit +TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT 1 5 No Hit +TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT 1 5 No Hit +TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA 1 5 No Hit +TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG 1 5 No Hit +TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT 1 5 No Hit +GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC 1 5 No Hit +CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT 1 5 No Hit +TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT 1 5 No Hit +TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA 1 5 No Hit +CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT 1 5 No Hit +GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA 1 5 No Hit +GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC 1 5 No Hit +CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA 1 5 No Hit +CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA 1 5 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG -1 0.0 0.0 0.0 0.0 0.0 0.0 -2 0.0 0.0 0.0 0.0 0.0 0.0 -3 0.0 0.0 0.0 0.0 0.0 0.0 -4 0.0 0.0 0.0 0.0 0.0 0.0 -5 0.0 0.0 0.0 0.0 0.0 0.0 -6 0.0 0.0 0.0 0.0 0.0 0.0 -7 0.0 0.0 0.0 0.0 0.0 0.0 -8 0.0 0.0 0.0 0.0 0.0 0.0 -9 0.0 0.0 0.0 0.0 0.0 0.0 -10 0.0 0.0 0.0 0.0 0.0 0.0 -11 0.0 0.0 0.0 0.0 0.0 0.0 -12 0.0 0.0 0.0 0.0 0.0 0.0 -13 0.0 0.0 0.0 0.0 0.0 0.0 -14 0.0 0.0 0.0 0.0 0.0 0.0 -15 0.0 0.0 0.0 0.0 0.0 0.0 -16 0.0 0.0 0.0 0.0 0.0 0.0 -17 0.0 0.0 0.0 0.0 0.0 0.0 -18 0.0 0.0 0.0 0.0 0.0 0.0 -19 0.0 0.0 0.0 0.0 0.0 0.0 -20 0.0 0.0 0.0 0.0 0.0 0.0 -21 0.0 0.0 0.0 0.0 0.0 0.0 -22 0.0 0.0 0.0 0.0 0.0 0.0 -23 0.0 0.0 0.0 0.0 0.0 0.0 -24 0.0 0.0 0.0 0.0 0.0 0.0 -25 0.0 0.0 0.0 0.0 0.0 0.0 -26 0.0 0.0 0.0 0.0 0.0 0.0 -27 0.0 0.0 0.0 0.0 0.0 0.0 -28 0.0 0.0 0.0 0.0 0.0 0.0 -29 0.0 0.0 0.0 0.0 0.0 0.0 -30 0.0 0.0 0.0 0.0 0.0 0.0 -31 0.0 0.0 0.0 0.0 0.0 0.0 -32 0.0 0.0 0.0 0.0 0.0 0.0 -33 0.0 0.0 0.0 0.0 0.0 0.0 -34 0.0 0.0 0.0 0.0 0.0 0.0 -35 0.0 0.0 0.0 0.0 0.0 0.0 -36 0.0 0.0 0.0 0.0 0.0 0.0 -37 0.0 0.0 0.0 0.0 0.0 0.0 -38 0.0 0.0 0.0 0.0 0.0 0.0 -39 0.0 0.0 0.0 0.0 0.0 0.0 -40 0.0 0.0 0.0 0.0 0.0 0.0 -41 0.0 0.0 0.0 0.0 0.0 0.0 -42 0.0 0.0 0.0 0.0 0.0 0.0 -43 0.0 0.0 0.0 0.0 0.0 0.0 -44 0.0 0.0 0.0 0.0 0.0 0.0 -45 0.0 0.0 0.0 0.0 0.0 0.0 -46 0.0 0.0 0.0 0.0 0.0 0.0 -47 0.0 0.0 0.0 0.0 0.0 0.0 -48 0.0 0.0 0.0 0.0 0.0 0.0 -49 0.0 0.0 0.0 0.0 0.0 0.0 -50 0.0 0.0 0.0 0.0 0.0 0.0 -51 0.0 0.0 0.0 0.0 0.0 0.0 -52 0.0 0.0 0.0 0.0 0.0 0.0 -53 0.0 0.0 0.0 0.0 0.0 0.0 -54 0.0 0.0 0.0 0.0 0.0 0.0 -55 0.0 0.0 0.0 0.0 0.0 0.0 -56 0.0 0.0 0.0 0.0 0.0 0.0 -57 0.0 0.0 0.0 0.0 0.0 0.0 -58 0.0 0.0 0.0 0.0 0.0 0.0 -59 0.0 0.0 0.0 0.0 0.0 0.0 +1 0 0 0 0 0 0 +2 0 0 0 0 0 0 +3 0 0 0 0 0 0 +4 0 0 0 0 0 0 +5 0 0 0 0 0 0 +6 0 0 0 0 0 0 +7 0 0 0 0 0 0 +8 0 0 0 0 0 0 +9 0 0 0 0 0 0 +10 0 0 0 0 0 0 +11 0 0 0 0 0 0 +12 0 0 0 0 0 0 +13 0 0 0 0 0 0 +14 0 0 0 0 0 0 +15 0 0 0 0 0 0 +16 0 0 0 0 0 0 +17 0 0 0 0 0 0 +18 0 0 0 0 0 0 +19 0 0 0 0 0 0 +20 0 0 0 0 0 0 +21 0 0 0 0 0 0 +22 0 0 0 0 0 0 +23 0 0 0 0 0 0 +24 0 0 0 0 0 0 +25 0 0 0 0 0 0 +26 0 0 0 0 0 0 +27 0 0 0 0 0 0 +28 0 0 0 0 0 0 +29 0 0 0 0 0 0 +30 0 0 0 0 0 0 +31 0 0 0 0 0 0 +32 0 0 0 0 0 0 +33 0 0 0 0 0 0 +34 0 0 0 0 0 0 +35 0 0 0 0 0 0 +36 0 0 0 0 0 0 +37 0 0 0 0 0 0 +38 0 0 0 0 0 0 +39 0 0 0 0 0 0 +40 0 0 0 0 0 0 +41 0 0 0 0 0 0 +42 0 0 0 0 0 0 +43 0 0 0 0 0 0 +44 0 0 0 0 0 0 +45 0 0 0 0 0 0 +46 0 0 0 0 0 0 +47 0 0 0 0 0 0 +48 0 0 0 0 0 0 +49 0 0 0 0 0 0 +50 0 0 0 0 0 0 +51 0 0 0 0 0 0 +52 0 0 0 0 0 0 +53 0 0 0 0 0 0 +54 0 0 0 0 0 0 +55 0 0 0 0 0 0 +56 0 0 0 0 0 0 +57 0 0 0 0 0 0 +58 0 0 0 0 0 0 +59 0 0 0 0 0 0 +60 0 0 0 0 0 0 +61 0 0 0 0 0 0 +62 0 0 0 0 0 0 +63 0 0 0 0 0 0 +64 0 0 0 0 0 0 +65 0 0 0 0 0 0 +66 0 0 0 0 0 0 +67 0 0 0 0 0 0 +68 0 0 0 0 0 0 +69 0 0 0 0 0 0 +70 0 0 0 0 0 0 >>END_MODULE diff --git a/tools/falco/test-data/fastqc_data_nogroup.txt b/tools/falco/test-data/fastqc_data_nogroup.txt index 842ada09b78..18ffb98f34e 100644 --- a/tools/falco/test-data/fastqc_data_nogroup.txt +++ b/tools/falco/test-data/fastqc_data_nogroup.txt @@ -1,4 +1,4 @@ -##Falco 1.2.3 +##Falco 1.2.4 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq @@ -1744,114 +1744,114 @@ Sequence length 1-108 #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672783 No Hit >>END_MODULE ->>Adapter Content warn +>>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG 1 0 0 0 0 0.0203874 0 -2 0 0 0 0 0.0815494 0 -3 0 0 0 0 0.142712 0 -4 0 0 0 0 0.183486 0 -5 0 0 0 0 0.285423 0 -6 0 0 0 0 0.38736 0 -7 0 0 0 0 0.489297 0 -8 0 0 0 0 0.591233 0 -9 0 0 0 0 0.672783 0 -10 0 0 0 0 0.754332 0 -11 0 0 0 0 0.835882 0 -12 0 0 0 0 0.917431 0 -13 0 0 0 0 1.01937 0 -14 0 0 0 0 1.1213 0 -15 0 0 0 0 1.24363 0 -16 0 0 0 0 1.34557 0 -17 0 0 0 0 1.46789 0 -18 0 0 0 0 1.59021 0 -19 0 0 0 0 1.67176 0 -20 0.122324 0 0 0 1.75331 0 -21 0.122324 0 0 0 1.83486 0 -22 0.122324 0 0 0 1.89602 0 -23 0.122324 0 0 0 1.95719 0 -24 0.122324 0 0 0 2.01835 0 -25 0.122324 0 0 0 2.07951 0 -26 0.122324 0 0 0 2.14067 0 -27 0.142712 0 0 0 2.20183 0 -28 0.183486 0 0 0 2.263 0 -29 0.224261 0 0 0 2.32416 0 -30 0.224261 0 0 0 2.38532 0 -31 0.224261 0 0 0 2.44648 0 -32 0.224261 0 0 0 2.50765 0 -33 0.224261 0 0 0 2.60958 0 -34 0.224261 0 0 0 2.71152 0 -35 0.265036 0 0 0 2.81346 0 -36 0.285423 0 0 0 2.89501 0 -37 0.326198 0 0 0 2.99694 0 -38 0.407747 0 0 0 3.09888 0 -39 0.468909 0 0 0 3.20082 0 -40 0.468909 0 0 0 3.30275 0 -41 0.468909 0 0 0 3.40469 0 -42 0.468909 0 0 0 3.48624 0 -43 0.468909 0 0 0 3.56779 0 -44 0.468909 0 0 0 3.60856 0 -45 0.468909 0 0 0 3.62895 0 -46 0.468909 0 0 0 3.64934 0 -47 0.468909 0 0 0 3.66972 0 -48 0.468909 0 0 0 3.69011 0 -49 0.468909 0 0 0 3.7105 0 -50 0.468909 0 0 0 3.7105 0 -51 0.468909 0 0 0 3.7105 0 -52 0.468909 0 0 0 3.7105 0 -53 0.468909 0 0 0 3.7105 0 -54 0.468909 0 0 0 3.7105 0 -55 0.468909 0 0 0 3.7105 0 -56 0.468909 0 0 0 3.7105 0 -57 0.468909 0 0 0 3.7105 0 -58 0.468909 0 0 0 3.7105 0 -59 0.468909 0 0 0 3.73089 0 -60 0.468909 0 0 0 3.75127 0 -61 0.468909 0 0 0 3.77166 0 -62 0.468909 0 0 0 3.81244 0 -63 0.468909 0 0 0 3.85321 0 -64 0.468909 0 0 0 3.89399 0 -65 0.468909 0 0 0 3.93476 0 -66 0.468909 0 0 0 3.97554 0 -67 0.468909 0 0 0 4.01631 0 -68 0.468909 0 0 0 4.05708 0 -69 0.468909 0 0 0 4.09786 0 -70 0.468909 0 0 0 4.13863 0 -71 0.468909 0 0 0 4.17941 0 -72 0.468909 0 0 0 4.22018 0 -73 0.468909 0 0 0 4.26096 0 -74 0.489297 0 0 0 4.32212 0 -75 0.489297 0 0 0 4.38328 0 -76 0.489297 0 0 0 4.42406 0 -77 0.489297 0 0 0 4.46483 0 -78 0.489297 0 0 0 4.50561 0 -79 0.489297 0 0 0 4.54638 0 -80 0.489297 0 0 0 4.58716 0 -81 0.489297 0 0 0 4.62793 0 -82 0.489297 0 0 0 4.66871 0 -83 0.509684 0 0 0 4.70948 0 -84 0.509684 0 0 0 4.75025 0 -85 0.509684 0 0 0 4.79103 0 -86 0.509684 0 0 0 4.8318 0 -87 0.509684 0 0 0 4.91335 0 -88 0.509684 0 0 0 4.9949 0 -89 0.509684 0 0 0 5.05607 0 -90 0.509684 0 0 0 5.09684 0 -91 0.509684 0 0 0 5.158 0 -92 0.570846 0 0 0 5.21916 0 -93 0.632008 0 0 0 5.28033 0 -94 0.632008 0 0 0 5.34149 0 -95 0.632008 0 0 0 5.40265 0 -96 0.632008 0 0 0 5.46381 0 -97 0.632008 0 0 0 5.52497 0 -98 0.632008 0 0 0 5.52497 0 -99 0.632008 0 0 0 5.52497 0 -100 0.632008 0 0 0 5.52497 0 -101 0.632008 0 0 0 5.52497 0 -102 0.632008 0 0 0 5.52497 0 -103 0.632008 0 0 0 5.52497 0 -104 0.632008 0 0 0 5.52497 0 -105 0.632008 0 0 0 5.52497 0 -106 0.632008 0 0 0 5.52497 0 -107 0.632008 0 0 0 5.52497 0 -108 0.632008 0 0 0 5.52497 0 +2 0 0 0 0 0.0611621 0 +3 0 0 0 0 0.0611621 0 +4 0 0 0 0 0.0611621 0 +5 0 0 0 0 0.122324 0 +6 0 0 0 0 0.122324 0 +7 0 0 0 0 0.122324 0 +8 0 0 0 0 0.142712 0 +9 0 0 0 0 0.142712 0 +10 0 0 0 0 0.142712 0 +11 0 0 0 0 0.142712 0 +12 0 0 0 0 0.142712 0 +13 0 0 0 0 0.163099 0 +14 0 0 0 0 0.163099 0 +15 0 0 0 0 0.183486 0 +16 0 0 0 0 0.203874 0 +17 0 0 0 0 0.224261 0 +18 0 0 0 0 0.224261 0 +19 0 0 0 0 0.224261 0 +20 0.122324 0 0 0 0.244648 0 +21 0.122324 0 0 0 0.244648 0 +22 0.122324 0 0 0 0.244648 0 +23 0.122324 0 0 0 0.244648 0 +24 0.122324 0 0 0 0.244648 0 +25 0.122324 0 0 0 0.244648 0 +26 0.122324 0 0 0 0.244648 0 +27 0.142712 0 0 0 0.244648 0 +28 0.183486 0 0 0 0.244648 0 +29 0.224261 0 0 0 0.244648 0 +30 0.224261 0 0 0 0.244648 0 +31 0.224261 0 0 0 0.244648 0 +32 0.224261 0 0 0 0.244648 0 +33 0.224261 0 0 0 0.285423 0 +34 0.224261 0 0 0 0.285423 0 +35 0.265036 0 0 0 0.30581 0 +36 0.285423 0 0 0 0.30581 0 +37 0.326198 0 0 0 0.326198 0 +38 0.407747 0 0 0 0.326198 0 +39 0.468909 0 0 0 0.326198 0 +40 0.468909 0 0 0 0.326198 0 +41 0.468909 0 0 0 0.326198 0 +42 0.468909 0 0 0 0.326198 0 +43 0.468909 0 0 0 0.326198 0 +44 0.468909 0 0 0 0.326198 0 +45 0.468909 0 0 0 0.326198 0 +46 0.468909 0 0 0 0.326198 0 +47 0.468909 0 0 0 0.326198 0 +48 0.468909 0 0 0 0.326198 0 +49 0.468909 0 0 0 0.326198 0 +50 0.468909 0 0 0 0.326198 0 +51 0.468909 0 0 0 0.326198 0 +52 0.468909 0 0 0 0.326198 0 +53 0.468909 0 0 0 0.326198 0 +54 0.468909 0 0 0 0.326198 0 +55 0.468909 0 0 0 0.326198 0 +56 0.468909 0 0 0 0.326198 0 +57 0.468909 0 0 0 0.326198 0 +58 0.468909 0 0 0 0.326198 0 +59 0.468909 0 0 0 0.326198 0 +60 0.468909 0 0 0 0.326198 0 +61 0.468909 0 0 0 0.326198 0 +62 0.468909 0 0 0 0.326198 0 +63 0.468909 0 0 0 0.326198 0 +64 0.468909 0 0 0 0.326198 0 +65 0.468909 0 0 0 0.326198 0 +66 0.468909 0 0 0 0.326198 0 +67 0.468909 0 0 0 0.326198 0 +68 0.468909 0 0 0 0.326198 0 +69 0.468909 0 0 0 0.326198 0 +70 0.468909 0 0 0 0.326198 0 +71 0.468909 0 0 0 0.326198 0 +72 0.468909 0 0 0 0.326198 0 +73 0.468909 0 0 0 0.326198 0 +74 0.468909 0 0 0 0.326198 0 +75 0.468909 0 0 0 0.326198 0 +76 0.468909 0 0 0 0.326198 0 +77 0.468909 0 0 0 0.326198 0 +78 0.468909 0 0 0 0.326198 0 +79 0.468909 0 0 0 0.326198 0 +80 0.468909 0 0 0 0.326198 0 +81 0.468909 0 0 0 0.326198 0 +82 0.468909 0 0 0 0.326198 0 +83 0.468909 0 0 0 0.326198 0 +84 0.468909 0 0 0 0.326198 0 +85 0.468909 0 0 0 0.326198 0 +86 0.468909 0 0 0 0.326198 0 +87 0.468909 0 0 0 0.326198 0 +88 0.468909 0 0 0 0.326198 0 +89 0.468909 0 0 0 0.326198 0 +90 0.468909 0 0 0 0.326198 0 +91 0.468909 0 0 0 0.326198 0 +92 0.468909 0 0 0 0.326198 0 +93 0.468909 0 0 0 0.326198 0 +94 0.468909 0 0 0 0.326198 0 +95 0.468909 0 0 0 0.326198 0 +96 0.468909 0 0 0 0.326198 0 +97 0.468909 0 0 0 0.326198 0 +98 0.468909 0 0 0 0.326198 0 +99 0.468909 0 0 0 0.326198 0 +100 0.468909 0 0 0 0.326198 0 +101 0.468909 0 0 0 0.326198 0 +102 0.468909 0 0 0 0.326198 0 +103 0.468909 0 0 0 0.326198 0 +104 0.468909 0 0 0 0.326198 0 +105 0.468909 0 0 0 0.326198 0 +106 0.468909 0 0 0 0.326198 0 +107 0.468909 0 0 0 0.326198 0 +108 0.468909 0 0 0 0.326198 0 >>END_MODULE diff --git a/tools/falco/test-data/fastqc_data_nogroup_summary.txt b/tools/falco/test-data/fastqc_data_nogroup_summary.txt deleted file mode 100644 index 7e94fefb156..00000000000 --- a/tools/falco/test-data/fastqc_data_nogroup_summary.txt +++ /dev/null @@ -1,11 +0,0 @@ -PASS Basic Statistics 1000trimmed_fastq -PASS Per base sequence quality 1000trimmed_fastq -FAIL Per tile sequence quality 1000trimmed_fastq -PASS Per sequence quality scores 1000trimmed_fastq -FAIL Per base sequence content 1000trimmed_fastq -WARN Per sequence GC content 1000trimmed_fastq -PASS Per base N content 1000trimmed_fastq -WARN Sequence Length Distribution 1000trimmed_fastq -PASS Sequence Duplication Levels 1000trimmed_fastq -WARN Overrepresented sequences 1000trimmed_fastq -WARN Adapter Content 1000trimmed_fastq diff --git a/tools/falco/test-data/fastqc_data_adapters_summary.txt b/tools/falco/test-data/fastqc_data_summary.txt similarity index 100% rename from tools/falco/test-data/fastqc_data_adapters_summary.txt rename to tools/falco/test-data/fastqc_data_summary.txt diff --git a/tools/falco/test-data/fastqc_report.html b/tools/falco/test-data/fastqc_report.html deleted file mode 100644 index 611aa925db4..00000000000 --- a/tools/falco/test-data/fastqc_report.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report

Report
Sun Sep 1 15:39:03 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : warn

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_adapters.html b/tools/falco/test-data/fastqc_report_adapters.html deleted file mode 100644 index 183af248509..00000000000 --- a/tools/falco/test-data/fastqc_report_adapters.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:39:42 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : pass

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_bisulfite.html b/tools/falco/test-data/fastqc_report_bisulfite.html deleted file mode 100644 index bab408df38a..00000000000 --- a/tools/falco/test-data/fastqc_report_bisulfite.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:40:53 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : warn

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : warn

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_bisulfite.txt b/tools/falco/test-data/fastqc_report_bisulfite.txt index f8d32038dd3..6b767d2c476 100644 --- a/tools/falco/test-data/fastqc_report_bisulfite.txt +++ b/tools/falco/test-data/fastqc_report_bisulfite.txt @@ -1,4 +1,4 @@ -##Falco 1.2.3 +##Falco 1.2.4 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq @@ -1597,114 +1597,114 @@ Sequence length 1-108 #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672783 No Hit >>END_MODULE ->>Adapter Content warn +>>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG 1 0 0 0 0 0.0203874 0 -2 0 0 0 0 0.0815494 0 -3 0 0 0 0 0.142712 0 -4 0 0 0 0 0.183486 0 -5 0 0 0 0 0.285423 0 -6 0 0 0 0 0.38736 0 -7 0 0 0 0 0.489297 0 -8 0 0 0 0 0.591233 0 -9 0 0 0 0 0.672783 0 -10 0 0 0 0 0.754332 0 -11 0 0 0 0 0.835882 0 -12 0 0 0 0 0.917431 0 -13 0 0 0 0 1.01937 0 -14 0 0 0 0 1.1213 0 -15 0 0 0 0 1.24363 0 -16 0 0 0 0 1.34557 0 -17 0 0 0 0 1.46789 0 -18 0 0 0 0 1.59021 0 -19 0 0 0 0 1.67176 0 -20 0.122324 0 0 0 1.75331 0 -21 0.122324 0 0 0 1.83486 0 -22 0.122324 0 0 0 1.89602 0 -23 0.122324 0 0 0 1.95719 0 -24 0.122324 0 0 0 2.01835 0 -25 0.122324 0 0 0 2.07951 0 -26 0.122324 0 0 0 2.14067 0 -27 0.142712 0 0 0 2.20183 0 -28 0.183486 0 0 0 2.263 0 -29 0.224261 0 0 0 2.32416 0 -30 0.224261 0 0 0 2.38532 0 -31 0.224261 0 0 0 2.44648 0 -32 0.224261 0 0 0 2.50765 0 -33 0.224261 0 0 0 2.60958 0 -34 0.224261 0 0 0 2.71152 0 -35 0.265036 0 0 0 2.81346 0 -36 0.285423 0 0 0 2.89501 0 -37 0.326198 0 0 0 2.99694 0 -38 0.407747 0 0 0 3.09888 0 -39 0.468909 0 0 0 3.20082 0 -40 0.468909 0 0 0 3.30275 0 -41 0.468909 0 0 0 3.40469 0 -42 0.468909 0 0 0 3.48624 0 -43 0.468909 0 0 0 3.56779 0 -44 0.468909 0 0 0 3.60856 0 -45 0.468909 0 0 0 3.62895 0 -46 0.468909 0 0 0 3.64934 0 -47 0.468909 0 0 0 3.66972 0 -48 0.468909 0 0 0 3.69011 0 -49 0.468909 0 0 0 3.7105 0 -50 0.468909 0 0 0 3.7105 0 -51 0.468909 0 0 0 3.7105 0 -52 0.468909 0 0 0 3.7105 0 -53 0.468909 0 0 0 3.7105 0 -54 0.468909 0 0 0 3.7105 0 -55 0.468909 0 0 0 3.7105 0 -56 0.468909 0 0 0 3.7105 0 -57 0.468909 0 0 0 3.7105 0 -58 0.468909 0 0 0 3.7105 0 -59 0.468909 0 0 0 3.73089 0 -60 0.468909 0 0 0 3.75127 0 -61 0.468909 0 0 0 3.77166 0 -62 0.468909 0 0 0 3.81244 0 -63 0.468909 0 0 0 3.85321 0 -64 0.468909 0 0 0 3.89399 0 -65 0.468909 0 0 0 3.93476 0 -66 0.468909 0 0 0 3.97554 0 -67 0.468909 0 0 0 4.01631 0 -68 0.468909 0 0 0 4.05708 0 -69 0.468909 0 0 0 4.09786 0 -70 0.468909 0 0 0 4.13863 0 -71 0.468909 0 0 0 4.17941 0 -72 0.468909 0 0 0 4.22018 0 -73 0.468909 0 0 0 4.26096 0 -74 0.489297 0 0 0 4.32212 0 -75 0.489297 0 0 0 4.38328 0 -76 0.489297 0 0 0 4.42406 0 -77 0.489297 0 0 0 4.46483 0 -78 0.489297 0 0 0 4.50561 0 -79 0.489297 0 0 0 4.54638 0 -80 0.489297 0 0 0 4.58716 0 -81 0.489297 0 0 0 4.62793 0 -82 0.489297 0 0 0 4.66871 0 -83 0.509684 0 0 0 4.70948 0 -84 0.509684 0 0 0 4.75025 0 -85 0.509684 0 0 0 4.79103 0 -86 0.509684 0 0 0 4.8318 0 -87 0.509684 0 0 0 4.91335 0 -88 0.509684 0 0 0 4.9949 0 -89 0.509684 0 0 0 5.05607 0 -90 0.509684 0 0 0 5.09684 0 -91 0.509684 0 0 0 5.158 0 -92 0.570846 0 0 0 5.21916 0 -93 0.632008 0 0 0 5.28033 0 -94 0.632008 0 0 0 5.34149 0 -95 0.632008 0 0 0 5.40265 0 -96 0.632008 0 0 0 5.46381 0 -97 0.632008 0 0 0 5.52497 0 -98 0.632008 0 0 0 5.52497 0 -99 0.632008 0 0 0 5.52497 0 -100 0.632008 0 0 0 5.52497 0 -101 0.632008 0 0 0 5.52497 0 -102 0.632008 0 0 0 5.52497 0 -103 0.632008 0 0 0 5.52497 0 -104 0.632008 0 0 0 5.52497 0 -105 0.632008 0 0 0 5.52497 0 -106 0.632008 0 0 0 5.52497 0 -107 0.632008 0 0 0 5.52497 0 -108 0.632008 0 0 0 5.52497 0 +2 0 0 0 0 0.0611621 0 +3 0 0 0 0 0.0611621 0 +4 0 0 0 0 0.0611621 0 +5 0 0 0 0 0.122324 0 +6 0 0 0 0 0.122324 0 +7 0 0 0 0 0.122324 0 +8 0 0 0 0 0.142712 0 +9 0 0 0 0 0.142712 0 +10 0 0 0 0 0.142712 0 +11 0 0 0 0 0.142712 0 +12 0 0 0 0 0.142712 0 +13 0 0 0 0 0.163099 0 +14 0 0 0 0 0.163099 0 +15 0 0 0 0 0.183486 0 +16 0 0 0 0 0.203874 0 +17 0 0 0 0 0.224261 0 +18 0 0 0 0 0.224261 0 +19 0 0 0 0 0.224261 0 +20 0.122324 0 0 0 0.244648 0 +21 0.122324 0 0 0 0.244648 0 +22 0.122324 0 0 0 0.244648 0 +23 0.122324 0 0 0 0.244648 0 +24 0.122324 0 0 0 0.244648 0 +25 0.122324 0 0 0 0.244648 0 +26 0.122324 0 0 0 0.244648 0 +27 0.142712 0 0 0 0.244648 0 +28 0.183486 0 0 0 0.244648 0 +29 0.224261 0 0 0 0.244648 0 +30 0.224261 0 0 0 0.244648 0 +31 0.224261 0 0 0 0.244648 0 +32 0.224261 0 0 0 0.244648 0 +33 0.224261 0 0 0 0.285423 0 +34 0.224261 0 0 0 0.285423 0 +35 0.265036 0 0 0 0.30581 0 +36 0.285423 0 0 0 0.30581 0 +37 0.326198 0 0 0 0.326198 0 +38 0.407747 0 0 0 0.326198 0 +39 0.468909 0 0 0 0.326198 0 +40 0.468909 0 0 0 0.326198 0 +41 0.468909 0 0 0 0.326198 0 +42 0.468909 0 0 0 0.326198 0 +43 0.468909 0 0 0 0.326198 0 +44 0.468909 0 0 0 0.326198 0 +45 0.468909 0 0 0 0.326198 0 +46 0.468909 0 0 0 0.326198 0 +47 0.468909 0 0 0 0.326198 0 +48 0.468909 0 0 0 0.326198 0 +49 0.468909 0 0 0 0.326198 0 +50 0.468909 0 0 0 0.326198 0 +51 0.468909 0 0 0 0.326198 0 +52 0.468909 0 0 0 0.326198 0 +53 0.468909 0 0 0 0.326198 0 +54 0.468909 0 0 0 0.326198 0 +55 0.468909 0 0 0 0.326198 0 +56 0.468909 0 0 0 0.326198 0 +57 0.468909 0 0 0 0.326198 0 +58 0.468909 0 0 0 0.326198 0 +59 0.468909 0 0 0 0.326198 0 +60 0.468909 0 0 0 0.326198 0 +61 0.468909 0 0 0 0.326198 0 +62 0.468909 0 0 0 0.326198 0 +63 0.468909 0 0 0 0.326198 0 +64 0.468909 0 0 0 0.326198 0 +65 0.468909 0 0 0 0.326198 0 +66 0.468909 0 0 0 0.326198 0 +67 0.468909 0 0 0 0.326198 0 +68 0.468909 0 0 0 0.326198 0 +69 0.468909 0 0 0 0.326198 0 +70 0.468909 0 0 0 0.326198 0 +71 0.468909 0 0 0 0.326198 0 +72 0.468909 0 0 0 0.326198 0 +73 0.468909 0 0 0 0.326198 0 +74 0.468909 0 0 0 0.326198 0 +75 0.468909 0 0 0 0.326198 0 +76 0.468909 0 0 0 0.326198 0 +77 0.468909 0 0 0 0.326198 0 +78 0.468909 0 0 0 0.326198 0 +79 0.468909 0 0 0 0.326198 0 +80 0.468909 0 0 0 0.326198 0 +81 0.468909 0 0 0 0.326198 0 +82 0.468909 0 0 0 0.326198 0 +83 0.468909 0 0 0 0.326198 0 +84 0.468909 0 0 0 0.326198 0 +85 0.468909 0 0 0 0.326198 0 +86 0.468909 0 0 0 0.326198 0 +87 0.468909 0 0 0 0.326198 0 +88 0.468909 0 0 0 0.326198 0 +89 0.468909 0 0 0 0.326198 0 +90 0.468909 0 0 0 0.326198 0 +91 0.468909 0 0 0 0.326198 0 +92 0.468909 0 0 0 0.326198 0 +93 0.468909 0 0 0 0.326198 0 +94 0.468909 0 0 0 0.326198 0 +95 0.468909 0 0 0 0.326198 0 +96 0.468909 0 0 0 0.326198 0 +97 0.468909 0 0 0 0.326198 0 +98 0.468909 0 0 0 0.326198 0 +99 0.468909 0 0 0 0.326198 0 +100 0.468909 0 0 0 0.326198 0 +101 0.468909 0 0 0 0.326198 0 +102 0.468909 0 0 0 0.326198 0 +103 0.468909 0 0 0 0.326198 0 +104 0.468909 0 0 0 0.326198 0 +105 0.468909 0 0 0 0.326198 0 +106 0.468909 0 0 0 0.326198 0 +107 0.468909 0 0 0 0.326198 0 +108 0.468909 0 0 0 0.326198 0 >>END_MODULE diff --git a/tools/falco/test-data/fastqc_report_bisulfite_summary.txt b/tools/falco/test-data/fastqc_report_bisulfite_summary.txt index 4281c854696..dfd9f170b57 100644 --- a/tools/falco/test-data/fastqc_report_bisulfite_summary.txt +++ b/tools/falco/test-data/fastqc_report_bisulfite_summary.txt @@ -8,4 +8,4 @@ PASS Per base N content 1000trimmed_fastq WARN Sequence Length Distribution 1000trimmed_fastq PASS Sequence Duplication Levels 1000trimmed_fastq WARN Overrepresented sequences 1000trimmed_fastq -WARN Adapter Content 1000trimmed_fastq +PASS Adapter Content 1000trimmed_fastq diff --git a/tools/falco/test-data/fastqc_report_contaminants.html b/tools/falco/test-data/fastqc_report_contaminants.html deleted file mode 100644 index d7a95504ae5..00000000000 --- a/tools/falco/test-data/fastqc_report_contaminants.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:39:23 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : warn

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_customlimits.html b/tools/falco/test-data/fastqc_report_customlimits.html deleted file mode 100644 index b923bc5f79b..00000000000 --- a/tools/falco/test-data/fastqc_report_customlimits.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:40:01 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : warn

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_hisat.html b/tools/falco/test-data/fastqc_report_hisat.html deleted file mode 100644 index 507f4a078f8..00000000000 --- a/tools/falco/test-data/fastqc_report_hisat.html +++ /dev/null @@ -1,187 +0,0 @@ -hisat_output_1_bam FastQC Report
FastQCFastQC Report
Thu 8 Jun 2023
hisat_output_1_bam

Summary

[OK]Basic Statistics

MeasureValue
Filenamehisat_output_1_bam
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences20
Total Bases1.4 kbp
Sequences flagged as poor quality0
Sequence length70
%GC43

[OK]Per base sequence quality

Per base quality graph

[FAIL]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[OK]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAG15.0No Hit
TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTA15.0No Hit
ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAG15.0No Hit
TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATG15.0No Hit
CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGT15.0No Hit
TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTC15.0No Hit
CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTT15.0No Hit
TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAG15.0No Hit
CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAG15.0No Hit
GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAG15.0No Hit
CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTAT15.0No Hit
GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAA15.0No Hit
GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAG15.0No Hit
CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCAC15.0No Hit
TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACC15.0No Hit
CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATA15.0No Hit
TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAG15.0No Hit
GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGA15.0No Hit
TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATT15.0No Hit
CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAA15.0No Hit

[OK]Adapter Content

Adapter graph

Produced by FastQC (version 0.12.1)
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_kmer.html b/tools/falco/test-data/fastqc_report_kmer.html deleted file mode 100644 index e4a5cb59dcf..00000000000 --- a/tools/falco/test-data/fastqc_report_kmer.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Mon May 27 16:59:30 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : pass

Falco 1.2.2
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_min_length.html b/tools/falco/test-data/fastqc_report_min_length.html deleted file mode 100644 index d9309493339..00000000000 --- a/tools/falco/test-data/fastqc_report_min_length.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Mon May 27 17:01:42 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : pass

Falco 1.2.2
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_nogroup.html b/tools/falco/test-data/fastqc_report_nogroup.html deleted file mode 100644 index 444964c36d3..00000000000 --- a/tools/falco/test-data/fastqc_report_nogroup.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:40:19 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : warn

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_reverse_complement.html b/tools/falco/test-data/fastqc_report_reverse_complement.html deleted file mode 100644 index 47057a8fc44..00000000000 --- a/tools/falco/test-data/fastqc_report_reverse_complement.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:41:08 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : warn

SequenceCountPercentagePossible Source
ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT330.672783No Hit

Adapter Content : warn

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_reverse_complement.txt b/tools/falco/test-data/fastqc_report_reverse_complement.txt index 4cd55952a12..e47fcd7b37c 100644 --- a/tools/falco/test-data/fastqc_report_reverse_complement.txt +++ b/tools/falco/test-data/fastqc_report_reverse_complement.txt @@ -1,4 +1,4 @@ -##Falco 1.2.3 +##Falco 1.2.4 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq @@ -1597,114 +1597,114 @@ Sequence length 1-108 #Sequence Count Percentage Possible Source ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT 33 0.672783 No Hit >>END_MODULE ->>Adapter Content warn +>>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG 1 0 0 0 0 0.0203874 0 -2 0 0 0 0 0.0815494 0 -3 0 0 0 0 0.142712 0 -4 0 0 0 0 0.183486 0 -5 0 0 0 0 0.285423 0 -6 0 0 0 0 0.38736 0 -7 0 0 0 0 0.489297 0 -8 0 0 0 0 0.591233 0 -9 0 0 0 0 0.672783 0 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0 -47 0.468909 0 0 0 3.66972 0 -48 0.468909 0 0 0 3.69011 0 -49 0.468909 0 0 0 3.7105 0 -50 0.468909 0 0 0 3.7105 0 -51 0.468909 0 0 0 3.7105 0 -52 0.468909 0 0 0 3.7105 0 -53 0.468909 0 0 0 3.7105 0 -54 0.468909 0 0 0 3.7105 0 -55 0.468909 0 0 0 3.7105 0 -56 0.468909 0 0 0 3.7105 0 -57 0.468909 0 0 0 3.7105 0 -58 0.468909 0 0 0 3.7105 0 -59 0.468909 0 0 0 3.73089 0 -60 0.468909 0 0 0 3.75127 0 -61 0.468909 0 0 0 3.77166 0 -62 0.468909 0 0 0 3.81244 0 -63 0.468909 0 0 0 3.85321 0 -64 0.468909 0 0 0 3.89399 0 -65 0.468909 0 0 0 3.93476 0 -66 0.468909 0 0 0 3.97554 0 -67 0.468909 0 0 0 4.01631 0 -68 0.468909 0 0 0 4.05708 0 -69 0.468909 0 0 0 4.09786 0 -70 0.468909 0 0 0 4.13863 0 -71 0.468909 0 0 0 4.17941 0 -72 0.468909 0 0 0 4.22018 0 -73 0.468909 0 0 0 4.26096 0 -74 0.489297 0 0 0 4.32212 0 -75 0.489297 0 0 0 4.38328 0 -76 0.489297 0 0 0 4.42406 0 -77 0.489297 0 0 0 4.46483 0 -78 0.489297 0 0 0 4.50561 0 -79 0.489297 0 0 0 4.54638 0 -80 0.489297 0 0 0 4.58716 0 -81 0.489297 0 0 0 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b/tools/falco/test-data/fastqc_report_reverse_complement_summary.txt deleted file mode 100644 index 7e94fefb156..00000000000 --- a/tools/falco/test-data/fastqc_report_reverse_complement_summary.txt +++ /dev/null @@ -1,11 +0,0 @@ -PASS Basic Statistics 1000trimmed_fastq -PASS Per base sequence quality 1000trimmed_fastq -FAIL Per tile sequence quality 1000trimmed_fastq -PASS Per sequence quality scores 1000trimmed_fastq -FAIL Per base sequence content 1000trimmed_fastq -WARN Per sequence GC content 1000trimmed_fastq -PASS Per base N content 1000trimmed_fastq -WARN Sequence Length Distribution 1000trimmed_fastq -PASS Sequence Duplication Levels 1000trimmed_fastq -WARN Overrepresented sequences 1000trimmed_fastq -WARN Adapter Content 1000trimmed_fastq diff --git a/tools/falco/test-data/fastqc_report_subsample.html b/tools/falco/test-data/fastqc_report_subsample.html deleted file mode 100644 index b3fc3892e5a..00000000000 --- a/tools/falco/test-data/fastqc_report_subsample.html +++ /dev/null @@ -1,2 +0,0 @@ - 1000trimmed_fastq - report
Report
Sun Sep 1 15:40:37 2024 -
1000trimmed_fastq

Summary

Basic Statistics: pass

MeasureValue
Filename1000trimmed_fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences4905
Sequences Flagged As Poor Quality0
Sequence length1 - 108
%GC:41

Per base sequence quality: pass

Per tile sequence quality : fail

Per sequence quality scores : pass

Per base sequence content : fail

Per sequence GC content: warn

Per base N content : pass

Sequence Length Distribution : warn

Sequence Duplication Levels : pass

Overrepresented sequences : pass

No overrepresented sequences

Adapter Content : pass

Falco 1.2.3
\ No newline at end of file diff --git a/tools/falco/test-data/fastqc_report_subsample.txt b/tools/falco/test-data/fastqc_report_subsample.txt index 601284edbd7..e0059f22fea 100644 --- a/tools/falco/test-data/fastqc_report_subsample.txt +++ b/tools/falco/test-data/fastqc_report_subsample.txt @@ -1,4 +1,4 @@ -##Falco 1.2.3 +##Falco 1.2.4 >>Basic Statistics pass #Measure Value Filename 1000trimmed_fastq @@ -1593,110 +1593,110 @@ Sequence length 1-108 #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence PolyA PolyG 1 0 0 0 0 0 0 2 0 0 0 0 0.0203874 0 -3 0 0 0 0 0.0407747 0 -4 0 0 0 0 0.0407747 0 -5 0 0 0 0 0.0407747 0 -6 0 0 0 0 0.0407747 0 -7 0 0 0 0 0.0407747 0 -8 0 0 0 0 0.0407747 0 -9 0 0 0 0 0.0407747 0 -10 0 0 0 0 0.0407747 0 -11 0 0 0 0 0.0407747 0 -12 0 0 0 0 0.0407747 0 -13 0 0 0 0 0.0407747 0 -14 0 0 0 0 0.0407747 0 -15 0 0 0 0 0.0407747 0 -16 0 0 0 0 0.0407747 0 -17 0 0 0 0 0.0611621 0 -18 0 0 0 0 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0.0611621 0 0 0 0.0407747 0 +105 0.0611621 0 0 0 0.0407747 0 +106 0.0611621 0 0 0 0.0407747 0 +107 0.0611621 0 0 0 0.0407747 0 +108 0.0611621 0 0 0 0.0407747 0 >>END_MODULE diff --git a/tools/falco/test-data/summary.txt b/tools/falco/test-data/summary.txt deleted file mode 100644 index 109484ffc6f..00000000000 --- a/tools/falco/test-data/summary.txt +++ /dev/null @@ -1,11 +0,0 @@ -PASS Basic Statistics 1000trimmed_fastq -PASS Per base sequence quality 1000trimmed_fastq -FAIL Per tile sequence quality 1000trimmed_fastq -PASS Per sequence quality scores 1000trimmed_fastq -FAIL Per base sequence content 1000trimmed_fastq -WARN Per sequence GC content 1000trimmed_fastq -PASS Per base N content 1000trimmed_fastq -WARN Sequence Length Distribution 1000trimmed_fastq -PASS Sequence Duplication Levels 1000trimmed_fastq -WARN Overrepresented sequences 1000trimmed_fastq -PASS Adapter Content 1000trimmed_fastq From 2e644f8228c9adbe49a3379db5bc4204b288b16f Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 27 Sep 2024 13:24:37 +0200 Subject: [PATCH 32/36] Fix test regex --- tools/falco/falco.xml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/tools/falco/falco.xml b/tools/falco/falco.xml index 3f2de700cf4..3b648d77eb1 100644 --- a/tools/falco/falco.xml +++ b/tools/falco/falco.xml @@ -79,7 +79,7 @@ - + @@ -89,7 +89,7 @@ - + @@ -99,7 +99,7 @@ - + @@ -110,7 +110,7 @@ - + @@ -121,7 +121,7 @@ - + @@ -131,7 +131,7 @@ - + @@ -141,7 +141,7 @@ - + @@ -171,7 +171,7 @@ - + @@ -182,7 +182,7 @@ - + @@ -194,7 +194,7 @@ - + @@ -205,7 +205,7 @@ - + From 3930dde692c6f87709280c13c2fe28bbb29b15b9 Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 27 Sep 2024 13:33:27 +0200 Subject: [PATCH 33/36] Fix invalid test --- tools/falco/falco.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/falco/falco.xml b/tools/falco/falco.xml index 3b648d77eb1..97860d320cf 100644 --- a/tools/falco/falco.xml +++ b/tools/falco/falco.xml @@ -144,7 +144,7 @@ - + @@ -92,7 +93,8 @@ - + + @@ -102,7 +104,8 @@ - + + From 692e15aaffa88398c20fd108b806aaf31b1606db Mon Sep 17 00:00:00 2001 From: Wolfgang Maier Date: Fri, 27 Sep 2024 17:05:19 +0200 Subject: [PATCH 36/36] Fix reference to test file in test 7 --- tools/falco/falco.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/falco/falco.xml b/tools/falco/falco.xml index 45da042defe..9498236de5b 100644 --- a/tools/falco/falco.xml +++ b/tools/falco/falco.xml @@ -148,7 +148,7 @@ - +