Commit a2076bd3 authored by Thonier Florian's avatar Thonier Florian

fuse.py; add 2 args to decide to compute distributions and/or export it

link to #3902
parent d486478a
......@@ -862,6 +862,8 @@ 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('--only_disributions', '-D', action='store_true', help='export only distributions')
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)')
......@@ -1005,6 +1007,31 @@ def main():
os.unlink(fasta_file.name)
else :
jlist_fused.d["similarity"] = [];
LISTE_D = []
LIST_AXES = ["germline", "top", # "name"
"seg5", "seg4", "seg3",
"lenSeq", # "evalue", l'arrondir ?
"seg5_delRight", "seg3_delLeft", "seg4_delRight", "seg3_delLeft",
"insert_53", "insert_54", "insert_43",
#"seg5_stop", "seg3_start", "seg4_stop", "seg4_start",
"lenCDR3", # "cdr3_stop", "cdr3_start",
"productive" #"junction_start", "junction_stop",
]
for axe1 in LIST_AXES:
LISTE_D.append([axe1])
for axe2 in LIST_AXES:
if axe1 != axe2:
LISTE_D.append([axe1, axe2])
if args.distributions or args.only_disributions:
print("### Save distributions file")
jlist_fused.init_distrib(LISTE_D)
jlist_fused.compute_distribution(LISTE_D)
if args.only_disributions:
jlist_fused.save_distributions("distribs.json")
return
print("### Save merged file")
jlist_fused.save_json(args.output)
......
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