Merge pull request #283 from deeptools/updateDocBEDTools

Update doc BEDTools

README.md

@@ -56,6 +56,9 @@ Also, pyGenomeTracks can be installed using pip
 $ pip install pyGenomeTracks
 ```
 
+Since version 3.5, pyGenomeTracks uses BEDTools, don't forget to install it or load it into your environment
+
+
 If the latest version wants to be installed use:
 
 ```bash

docs/content/faq.rst

@@ -13,6 +13,16 @@ when you were providing ``cool`` file from `cooler balance <https://cooler.readt
 If you want to keep the old scale you need to downgrade to HiCMatrix version 12 but version 13 also correct some bugs so we advice
 to change your ``max_value`` in your parameter file to adjust to the new scale.
 
+No output generated with version 3.5 installed with pip
+-------------------------------------------------------
+If you used pyGenomeTracks version 3.5 and the last line you get is:
+
+.. code:: bash
+
+    INFO:pygenometracks.tracksClass:initialize x. [xxxxx]
+
+It is highly probable that BEDTools is not installed or not loaded in your environment.
+
 My Hi-C plot looks like no correction was applied when using cool matrix
 ------------------------------------------------------------------------
 pyGenomeTracks is using `HiCMatrix <https://github.com/deeptools/HiCMatrix>`_ to read the matrix from ``cool`` format.

docs/content/installation.rst

@@ -10,14 +10,22 @@ Remember -- pyGenomeTracks is available for **command line usage** as well as fo
 Requirements
 -------------
 
-* Python >=3.6
+Python dependencies:
+
+* Python >= 3.6
 * numpy >= 1.16
-* intervaltree >=2.1.0
-* pyBigWig >= 0.3.4
-* hicmatrix >= 0.14
-* pysam >= 0.8
-* matplotlib >= 3.1.1
-* gffutils >=0.9
+* intervaltree >= 2.1.0
+* pyBigWig >= 0.3.16
+* hicmatrix >= 15
+* pysam >= 0.14
+* matplotlib == 3.1.1
+* gffutils >= 0.9
+* pybedtools >= 0.8.1
+* tqdm >= 4.20
+
+External dependencies:
+
+* BEDTools
 
 Command line installation using ``conda``
 -----------------------------------------
@@ -44,6 +52,8 @@ Install pyGenomeTracks using the following command:
 
 All python requirements should be automatically installed.
 
+Since version 3.5, pyGenomeTracks require BEDTools, do not forget to install it or load it into your environment.
+
 If you need to specify a specific path for the installation of the tools, make use of `pip install`'s numerous options:
 
 .. code:: bash
@@ -55,7 +65,7 @@ Command line installation without ``pip``
 
 You are highly recommended to use `conda install` rather than the following complicated steps.
 
-1. Install the requirements listed above in the "requirements" section. This is done automatically by `pip`.
+1. Install the requirements listed above in the "requirements" section. This is done automatically by `pip` (except BEDTools).
 
 2. Download source code
 ::

pygenometracks/tests/test_bedGraphTrack.py

@@ -268,6 +268,14 @@ def test_plot_bedgraph_tracks_rasterize():
     ini_file = os.path.join(ROOT, "bedgraph_useMid.ini")
     region = "chr2:73,800,000-75,744,000"
     expected_file = os.path.join(ROOT, 'master_bedgraph_useMid.pdf')
+    # matplotlib compare on pdf will create a png next to it.
+    # To avoid issues related to write in test_data folder
+    # We copy the expected file into a temporary place
+    new_expected_file = NamedTemporaryFile(suffix='.pdf',
+                                           prefix='pyGenomeTracks_test_',
+                                           delete=False)
+    os.system(f'cp {expected_file} {new_expected_file.name}')
+    expected_file = new_expected_file.name
     args = f"--tracks {ini_file} --region {region} "\
            "--trackLabelFraction 0.2 --width 38 --dpi 130 "\
            f"--outFileName {outfile.name}".split()

pygenometracks/tests/test_hiCMatrixTracks.py

@@ -468,13 +468,19 @@ def test_plot_tracks_with_hic_rasterize_height_2chr():
         output_file = outfile.name[:-4] + '_' + region_str + extension
         expected_file = os.path.join(ROOT, 'master_plot_hic_rasterize_height_'
                                      + region_str + extension)
+        # matplotlib compare on pdf will create a png next to it.
+        # To avoid issues related to write in test_data folder
+        # We copy the expected file into a temporary place
+        new_expected_file = NamedTemporaryFile(suffix='.pdf',
+                                               prefix='pyGenomeTracks_test_',
+                                               delete=False)
+        os.system(f'cp {expected_file} {new_expected_file.name}')
+        expected_file = new_expected_file.name
         res = compare_images(expected_file,
                              output_file, tolerance)
         assert res is None, res
 
         os.remove(output_file)
-        if extension == '.pdf':
-            os.remove(expected_file.replace(extension, '_pdf.png'))
 
 
 def test_plot_tracks_with_hic_rasterize_height_2chr_individual():
@@ -485,15 +491,20 @@ def test_plot_tracks_with_hic_rasterize_height_2chr_individual():
                                      delete=False)
         expected_file = os.path.join(ROOT, 'master_plot_hic_rasterize_height_'
                                      + region.replace(':', '-') + extension)
-
+        # matplotlib compare on pdf will create a png next to it.
+        # To avoid issues related to write in test_data folder
+        # We copy the expected file into a temporary place
+        new_expected_file = NamedTemporaryFile(suffix='.pdf',
+                                               prefix='pyGenomeTracks_test_',
+                                               delete=False)
+        os.system(f'cp {expected_file} {new_expected_file.name}')
+        expected_file = new_expected_file.name
         args = f"--tracks {ini_file} --region {region} "\
                "--trackLabelFraction 0.23 --width 38 --dpi 10 "\
                f"--outFileName {outfile.name}".split()
         pygenometracks.plotTracks.main(args)
         res = compare_images(expected_file,
                              outfile.name, tolerance)
-        if extension == '.pdf':
-            os.remove(expected_file.replace(extension, '_pdf.png'))
     assert res is None, res