Other formats

scripts/opentims_extract_tdf.py

@@ -6,51 +6,109 @@
 from opentimspy import OpenTIMS
 
 if opentimspy.bruker_bridge_present:
-    all_columns = ('frame','scan','tof','intensity','mz','inv_ion_mobility','retention_time')
+    all_columns = (
+        "frame",
+        "scan",
+        "tof",
+        "intensity",
+        "mz",
+        "inv_ion_mobility",
+        "retention_time",
+    )
 else:
-    all_columns = ('frame','scan','tof','intensity','retention_time')
+    all_columns = ("frame", "scan", "tof", "intensity", "retention_time")
 
 import argparse
 
-parser = argparse.ArgumentParser(description='Export a set of frames in TSV format.')
+parser = argparse.ArgumentParser(description="Export a set of frames in TSV format.")
 parser.add_argument("path", help="TDF dataset path", type=Path)
-parser.add_argument("frames", help="Comma-separated list of frames, including ranges. Example: 314,320-330,435. Will output everything if omitted.", nargs='?', default="")
+parser.add_argument(
+    "frames",
+    help="Comma-separated list of frames, including ranges. Example: 314,320-330,435. Will output everything if omitted.",
+    nargs="?",
+    default="",
+)
 parser.add_argument("--no-hdr", help="Do not print the header.", action="store_true")
-parser.add_argument("-o", "--output", help="File to output to. Will print to stdout if omitted", type=Path, default=None)
-args=parser.parse_args()
+parser.add_argument(
+    "-o",
+    "--output",
+    help="File to output to. Will print to stdout if omitted",
+    type=Path,
+    default=None,
+)
+parser.add_argument(
+    "--format",
+    type=str,
+    help="Output format, one of: mmapped_df (fastest), hdf5, csv (default).",
+    required=False,
+    default="csv",
+)
 
+args = parser.parse_args()
+
+import tqdm
 
 frames = set()
 if args.frames != "":
-    for frame_desc in args.frames.split(','):
-        if '-' in frame_desc:
-            start, end = frame_desc.split('-')
-            frames.update(range(int(start), int(end)+1))
+    for frame_desc in args.frames.split(","):
+        if "-" in frame_desc:
+            start, end = frame_desc.split("-")
+            frames.update(range(int(start), int(end) + 1))
         else:
             frames.add(int(frame_desc))
 
 
-out_file = sys.stdout if args.output is None else args.output.open(mode="wt")
+if args.format == "mmapped_df":
+    try:
+        import mmapped_df
+    except ImportError:
+        print(
+            "mmapped_df is not installed. Please install it from https://github.com/michalsta/mmapped_df, or use a different format."
+        )
+        sys.exit(1)
+    opener = lambda: mmapped_df.DatasetWriter(args.output)
+    writer = lambda f, df: f.append(**df)
+elif args.format == "hdf5":
+    import pandas as pd
 
-with OpenTIMS(args.path) as D:
-    if args.frames == "":
-        frames = set(D.frames['Id'])
+    opener = lambda: pd.HDFStore(args.output, mode="w", complevel=9, complib="blosc")
+    writer = lambda f, df: pd.DataFrame(df).to_hdf(
+        f,
+        key="df",
+        format="table",
+        data_columns=True,
+        complevel=9,
+        complib="blosc",
+        append=True,
+    )
+elif args.format == "csv":
+    import pandas as pd
+
+    out_file = sys.stdout if args.output is None else args.output.open(mode="wt")
+    opener = lambda: out_file
+    hdr_written = False
+
+    def writer(f, df):
+        global hdr_written
+        df = pd.DataFrame(df)
+        df.to_csv(f, header=not hdr_written)
+        hdr_written = True
+
+else:
+    raise ValueError(
+        f"Invalid format: {args.format}. Please specify one of: mmapped_df, hdf5, csv."
+    )
 
-    # prepare and print the CSV header:
-    if not args.no_hdr:
-        header = '"' + '"\t"'.join(all_columns) + '"'
-        print(header, file=out_file)
 
+progressbar = lambda x: x
+if args.output != None:
+    progressbar = tqdm.tqdm
+
+with OpenTIMS(args.path) as D, opener() as f:
+    if args.frames == "":
+        frames = set(D.frames["Id"])
 
     # Iterate over frames. This will store only one frame at a time in RAM, preventing out of memory errors.
-    for frame_id in sorted(frames):
+    for frame_id in progressbar(list(sorted(frames))):
         frame = D.query(frame_id)
-        peak_idx = 0
-        # Frame is stored as a dict of column vectors
-        while peak_idx < len(frame['frame']):
-            row = [str(frame[colname][peak_idx]) for colname in all_columns]
-            print('\t'.join(row), file=out_file)
-            peak_idx += 1
-
-if args.output is not None:
-    out_file.close()
+        writer(f, frame)