Commit 2a36aad0 authored by Thonier Florian's avatar Thonier Florian
Browse files; add new options to get the list of all available axes, create all...; add new options to get the list of all available axes, create all distribution, or give axes for a specific distribution computing (with multiple call)
Link to #3944
parent 0e284056
......@@ -1040,8 +1040,6 @@ def main():
group_options.add_argument('--test', action='store_true', help='run self-tests')
group_options.add_argument('--multi', action='store_true', help='merge different systems from a same timepoint (deprecated, do not use)')
group_options.add_argument('--distributions', '-d', action='store_true', help='compute distributions')
group_options.add_argument('--no-clones', action='store_true', help='do not output individual clones')
group_options.add_argument('--compress', '-c', action='store_true', help='compress point names, removing common substrings')
group_options.add_argument('--pipeline', '-p', action='store_true', help='compress point names (internal Bonsai pipeline)')
......@@ -1054,7 +1052,10 @@ 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")
group_options.add_argument("--distributions", "-d", action='append', type=str, help="a set of axes for distribution computing; callable mutliple time")
group_options.add_argument('--distributions_all', '-D', action='store_true', default=False, help='compute a preset of distributions')
group_options.add_argument('--distributions_list', '-l', action='store_true', default=False, help='list the available axes for distributions')
group_options.add_argument('--no-clones', action='store_true', default=False, help='do not output individual clones')
parser.add_argument('file', nargs='+', help='''input files (.vidjil/.cnltab)''')
......@@ -1067,15 +1068,18 @@ def main():
jlist_fused = None
# 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.distributions_list == True:
print("### List of available axes for distributions:\n%s\n" % AVAILABLE_AXES)
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(","))
if args.distributions_all == True:
LIST_DISTRIBUTIONS = get_preset_of_distribution()
if args.distributions != None:
for elt in args.distributions:
axes = elt.split(",")
if axes not in LIST_DISTRIBUTIONS:
print("### -- " + DESCRIPTION)
......@@ -1162,7 +1166,7 @@ def main():
print('\t==> merge to', jlist_fused)
if args.distributions:
print("### Compute distributions")
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