Commit cf74a343 authored by Mathieu Giraud's avatar Mathieu Giraud

germline/split-from-imgt.py: handle custom 118 positions

parent 7d72e3b2
...@@ -130,15 +130,25 @@ CUSTOM_118 = { '': 0 # custom position of 118 in sequences without the Trp-Gl ...@@ -130,15 +130,25 @@ CUSTOM_118 = { '': 0 # custom position of 118 in sequences without the Trp-Gl
def gap_j(seq): def gap_j(seq):
'''Gap J sequences in order to align the Phe118/Trp118 codon''' '''Gap J sequences in order to align the Phe118/Trp118 codon'''
m = j118.search(seq)
if not m: seqs = seq.strip()
if len(seq) > PHE_TRP_WARN_SIZE:
print "# %s in %s" % (PHE_TRP_WARN_MSG, seq) if seqs in CUSTOM_118:
seq = "# %s\n%s" % (PHE_TRP_WARN_MSG, seq) print "# Custom 118 position in %s" % seq
return seq pos = CUSTOM_118[seqs]
seq = seq.replace('\n', " # Custom\n")
else:
m = j118.search(seq)
if not m:
if len(seq) > PHE_TRP_WARN_SIZE:
print "# %s in %s" % (PHE_TRP_WARN_MSG, seq)
seq = "# %s\n%s" % (PHE_TRP_WARN_MSG, seq)
return seq
pos = m.start() + 1 # positions start at 1
pos = m.start() + 1 # positions start at 1
return (MAX_GAP_J - pos) * '.' + seq return (MAX_GAP_J - pos) * '.' + seq
......
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