Commit 7732d520 authored by Mathieu Giraud's avatar Mathieu Giraud

imgt-to-vdj.py: further factorization between IMGT and MiXCR wrappers

parent dc0a51ff
...@@ -129,7 +129,8 @@ def header_vquest_results(ff_fasta, ff_vquest): ...@@ -129,7 +129,8 @@ def header_vquest_results(ff_fasta, ff_vquest):
while not vquest: while not vquest:
vquest = f_vquest.next().strip() vquest = f_vquest.next().strip()
yield (fasta, vquest) r = IMGT_VQUEST_Result(result)
yield (fasta.replace('>', ''), r.to_vdj())
def header_mixcr_results(ff_mixcr): def header_mixcr_results(ff_mixcr):
...@@ -148,17 +149,12 @@ def header_mixcr_results(ff_mixcr): ...@@ -148,17 +149,12 @@ def header_mixcr_results(ff_mixcr):
if __name__ == '__main__': if __name__ == '__main__':
if 'mixcr' in sys.argv[1]: if 'mixcr' in sys.argv[1]:
for (header, result) in header_mixcr_results(sys.argv[1]): gen = header_mixcr_results(sys.argv[1])
print "#%s" % header else:
print ">%s" % result gen = header_vquest_results(sys.argv[1], sys.argv[2])
print
# output .vdj data
sys.exit(0) for (header, result) in gen:
print "#%s" % header
for (header, result) in header_vquest_results(sys.argv[1], sys.argv[2]): print ">%s" % result
# print "=========="
print header.replace('>', '#')
r = IMGT_VQUEST_Result(result)
# print r
print ">%s" % r.to_vdj()
print print
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