Addition of download_pairwise_alignments_from_ucsc_seperate_files.py …

…script in ucsc_pairwise_alignments_custom_scripts/0.1

ucsc_pairwise_alignments_custom_scripts/0.1/Dockerfile

@@ -3,7 +3,7 @@ FROM python:3.6.5
 
 ##### METADATA #####
 LABEL base.image="python:3.6.5"
-LABEL version="2"
+LABEL version="3"
 LABEL software="ucsc_pairwise_alignments_custom_scripts"
 LABEL software.version="0.1"
 LABEL software.description="Custom scripts for ucsc alignments"

ucsc_pairwise_alignments_custom_scripts/0.1/download_pairwise_alignments_from_ucsc_seperate_files.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+
+__version__ = "0.1"
+__author__ = "Foivos Gypas"
+__contact__ = "[email protected]"
+__doc__ = "Download pairwise alignments from ucsc"
+
+# _____________________________________________________________________________
+# -----------------------------------------------------------------------------
+# import needed (external) modules
+# -----------------------------------------------------------------------------
+
+import sys
+import os
+from argparse import ArgumentParser, RawTextHelpFormatter
+
+# _____________________________________________________________________________
+# -----------------------------------------------------------------------------
+# Main function
+# -----------------------------------------------------------------------------
+
+
+def main():
+    """ Main function """
+
+    parser = ArgumentParser(
+        description=__doc__,
+        formatter_class=RawTextHelpFormatter
+    )
+
+    parser.add_argument(
+        "--organism",
+        dest="organism",
+        help="Reference organism (e.g. hg38, hg19, mm10)",
+        required=True,
+        metavar="FILE"
+    )
+
+    parser.add_argument(
+        "--organism_to_download",
+        dest="organism_to_download",
+        help="Name of pairwise alignment organism",
+        required=True
+    )
+
+    parser.add_argument(
+        "--out",
+        dest="out",
+        help="Output directory",
+        required=True,
+        metavar="FILE"
+    )
+
+    parser.add_argument(
+        "--verbose",
+        action="store_true",
+        dest="verbose",
+        default=False,
+        required=False,
+        help="Verbose"
+    )
+
+    parser.add_argument(
+        '--version',
+        action='version',
+        version=__version__
+    )
+
+    # _________________________________________________________________________
+    # -------------------------------------------------------------------------
+    # get the arguments
+    # -------------------------------------------------------------------------
+    try:
+        options = parser.parse_args()
+    except(Exception):
+        parser.print_help()
+
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(1)
+
+    start = "rsync://hgdownload.soe.ucsc.edu/goldenPath/" + options.organism + "/vs"
+    f_s_l = options.organism_to_download
+    f_s = f_s_l[0].upper() + f_s_l[1:]
+    output_dir = os.path.join(options.out, options.organism + "_to_" + f_s_l)
+    # file_name = options.organism + "." + f_s_l + ".net.axt.gz"
+    if not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+
+    download_link = start + f_s + "/axtNet/"
+
+    try:
+        if options.verbose:
+            sys.stdout.write("Downloading " + download_link + os.linesep)
+        os.system("rsync -a -P " + download_link + " " + output_dir)
+    except:
+        sys.stderr.write("Could not download " + download_link + os.linesep)
+
+# _____________________________________________________________________________
+# -----------------------------------------------------------------------------
+# Call the Main function and catch Keyboard interrups
+# -----------------------------------------------------------------------------
+
+
+if __name__ == '__main__':
+    try:
+        main()
+    except KeyboardInterrupt:
+        sys.stderr.write("User interrupt!" + os.linesep)
+        sys.exit(0)