Commit b1dda1f0 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Vidjil Team

scripts/ option -o, link sequences with their original filename

parent ca6d22a0
......@@ -12,6 +12,7 @@ parser.add_argument('--sequences', '-s', action='store_true', help='link sequen
parser.add_argument('--results', '-r', action='store_true', help='link results files')
parser.add_argument('--diag', '-d', action='store_true', help='link only diagnosis results (first sample per patient)')
parser.add_argument('--analysis', '-a', action='store_true', help='link analysis files (last file per patient)')
parser.add_argument('--original', '-o', action='store_true', help='for -s, use original filenames')
parser.add_argument('--filter', '-f', type=str, default='', help='filter on patient name or info (%(default)s), only for -s or -d')
parser.add_argument('--creator', '-c', type=int, default=0, help='filter on patient creator id, only for -s or -d')
parser.add_argument('--raw', '-w', action='store_true', help='do not link, only display the list of raw files')
......@@ -41,10 +42,15 @@ if args.sequences:
if res.patient.creator != args.creator:
our_id += 1
if args.original:
f = res.sequence_file.filename
our_id += 1
f = "%5s.fa" % our_id
link("%s/%-20s" % (defs.DIR_SEQUENCES, res.sequence_file.data_file),
"%5s.fa" % our_id,
"seq-%04d %-20s" % (, res.sequence_file.filename)
+ "\t# %s" % patient_string(res.patient),
not args.raw)
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