Commit 686bf290 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Marc Duez

fuse.py: orders 'systems_segmented' according to GERMLINES_ORDER

parent c10db250
...@@ -31,6 +31,12 @@ from operator import itemgetter ...@@ -31,6 +31,12 @@ from operator import itemgetter
VIDJIL_JSON_VERSION = "2014.02" VIDJIL_JSON_VERSION = "2014.02"
GERMLINES_ORDER = ['TRA', 'TRB', 'TRG', 'TRD', 'DD', 'IGH', 'DHJH', 'IJK', 'IJL']
def ordered(d, key=None):
'''sorts a dictionary into an OrderedDict'''
return collections.OrderedDict([(k, d[k]) for k in sorted(d, key=key)])
#### ####
class Window: class Window:
...@@ -733,6 +739,7 @@ def main(): ...@@ -733,6 +739,7 @@ def main():
print '\t==> merge to', jlist_fused print '\t==> merge to', jlist_fused
jlist_fused.d['germline'][0] = "multi" jlist_fused.d['germline'][0] = "multi"
jlist_fused.d["system_segmented"] = ordered(jlist_fused.d["system_segmented"], key=lambda sys: ((GERMLINES_ORDER + [sys]).index(sys), sys))
else: else:
print "### Read and merge input files" print "### Read and merge input files"
......
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