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Commit 8ffa2019 authored by Thonier Florian's avatar Thonier Florian; add an option to give the distributions to computes

Link to #3944
parent 577ce843
......@@ -936,10 +936,11 @@ def main():
group_options.add_argument('--pre', type=str,help='pre-process program (launched on each input .vidjil file) (needs defs.PRE_PROCESS_DIR)')
group_options.add_argument("--axes", "-a", action='append', help="Axes of distributions to compute; callable mutliple time")
parser.add_argument('file', nargs='+', help='''input files (.vidjil/.cnltab)''')
args = parser.parse_args()
# print args
if args.test:
import doctest
......@@ -949,21 +950,15 @@ def main():
jlist_fused = None
LIST_AXIS = ["germline",
"seg5", "seg4", "seg3",
"lenSeqConsensus", "lenSeqAverage",
"seg5_delRight", "seg3_delLeft", "seg4_delRight", "seg3_delLeft",
"insert_53", "insert_54", "insert_43",
for axis1 in LIST_AXIS:
for axis2 in LIST_AXIS:
if axis1 != axis2:
LIST_DISTRIBUTIONS.append([axis1, axis2])
# Available axes = germline, seg5, seg4, seg3, lenCDR3, lenSeqConsensus, lenSeqAverage, seg5_delRight, seg3_delLeft, seg4_delRight, seg3_delLeft, insert_53, insert_54, insert_43, productive
if args.axes != None:
if not args.distributions:
print( "No inclusions of distributions. Please add --distributions")
for elt in args.axes:
LIST_DISTRIBUTIONS.append( elt.split(","))
print("### -- " + DESCRIPTION)
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