Mercurial > repos > galaxyp > retrieve_ensembl_bed
diff retrieve_ensembl_bed.py @ 1:c3d600729b6f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1
| author | galaxyp |
|---|---|
| date | Mon, 22 Jan 2018 13:13:26 -0500 |
| parents | 887e111c0919 |
| children | e385fe93df68 |
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--- a/retrieve_ensembl_bed.py Sun Jan 14 14:11:53 2018 -0500 +++ b/retrieve_ensembl_bed.py Mon Jan 22 13:13:26 2018 -0500 @@ -12,6 +12,8 @@ #------------------------------------------------------------------------------ """ +from __future__ import print_function + import argparse import re import sys @@ -49,7 +51,6 @@ parser.add_argument('-v', '--verbose', action='store_true', help='Verbose') parser.add_argument('-d', '--debug', action='store_true', help='Debug') args = parser.parse_args() - # print >> sys.stderr, "args: %s" % args species = args.species out_wtr = open(args.output, 'w') if args.output != '-' else sys.stdout biotypes = ';'.join(['biotype=%s' % bt.strip() @@ -72,24 +73,24 @@ selected_regions[chrom] = [] selected_regions[chrom].append([start, end, strand]) if args.debug: - print >> sys.stderr, "selected_regions: %s" % selected_regions + print("selected_regions: %s" % selected_regions, file=sys.stderr) def retrieve_region(species, ref, start, stop, strand): transcript_count = 0 - regions = range(start, stop, max_region) + regions = list(range(start, stop, max_region)) if not regions or regions[-1] < stop: regions.append(stop) for end in regions[1:]: bedlines = get_transcripts_bed(species, ref, start, end, strand=strand, params=biotypes) if args.debug: - print >> sys.stderr,\ - "%s\t%s\tstart: %d\tend: %d\tcDNA transcripts:%d"\ - % (species, ref, start, end, len(bedlines)) + print("%s\t%s\tstart: %d\tend: %d\tcDNA transcripts:%d" % + (species, ref, start, end, len(bedlines)), + file=sys.stderr) # start, end, seq for i, bedline in enumerate(bedlines): if args.debug: - print >> sys.stderr, "%s\n" % (bedline) + print("%s\n" % (bedline), file=sys.stderr) if not args.ucsc_chrom_names: bedline = re.sub('^[^\t]+', ref, bedline) try: @@ -100,8 +101,8 @@ out_wtr.write("\n") out_wtr.flush() except Exception as e: - print >> sys.stderr,\ - "BED error (%s) : %s\n" % (e, bedline) + print("BED error (%s) : %s\n" % (e, bedline), + file=sys.stderr) start = end + 1 return transcript_count @@ -112,8 +113,8 @@ length = coord_systems['chromosome'][ref] ref_lengths[ref] = length if args.toplevel: - print >> sys.stderr,\ - "%s\t%s\tlength: %d" % (species, ref, length) + print("%s\t%s\tlength: %d" % (species, ref, length), + file=sys.stderr) if selected_regions: transcript_count = 0 for ref in sorted(selected_regions.keys()): @@ -129,10 +130,10 @@ strand) if args.debug or args.verbose: length = stop - start - print >> sys.stderr,\ - "%s\t%s:%d-%d%s\tlength: %d\ttrancripts:%d"\ - % (species, ref, start, stop, strand, - length, transcript_count) + print("%s\t%s:%d-%d%s\tlength: %d\ttrancripts:%d" % + (species, ref, start, stop, strand, + length, transcript_count), + file=sys.stderr) else: strand = '' start = 0 @@ -140,15 +141,14 @@ length = ref_lengths[ref] transcript_count = 0 if args.debug: - print >> sys.stderr,\ - "Retrieving transcripts: %s\t%s\tlength: %d"\ - % (species, ref, length) + print("Retrieving transcripts: %s\t%s\tlength: %d" % + (species, ref, length), file=sys.stderr) transcript_count += retrieve_region(species, ref, start, length, strand) if args.debug or args.verbose: - print >> sys.stderr,\ - "%s\t%s\tlength: %d\ttrancripts:%d"\ - % (species, ref, length, transcript_count) + print("%s\t%s\tlength: %d\ttrancripts:%d" % + (species, ref, length, transcript_count), + file=sys.stderr) if __name__ == "__main__":