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Accounting for the possibility of a delete-state in function check_for_j. #10

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Accounting for the possibility of a delete-state in function check_for_j. #10

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6 changes: 5 additions & 1 deletion lib/python/anarci/anarci.py
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Original file line number Diff line number Diff line change
Expand Up @@ -741,7 +741,11 @@ def check_for_j( sequences, alignments, scheme ):
# Sandwich the presumed CDR3 region between the V and J regions.

vRegion = ali[:cys_ai+1]
jRegion = [ (state, index+cys_si+1) for state, index in re_states[0] if state[0] >= 117 ]
# jRegion = [ (state, index+cys_si+1) for state, index in re_states[0] if state[0] >= 117 ]
# HMM may assign a "delete" state (see function _hmm_alignment_to_states), in which case the
# position index is None and the expression index+cys_si+1 will fail. A good solution seems
# to skip such states, because they do not correspond to a position in the sequence anyway.
jRegion = [ (state, index+cys_si+1) for state, index in re_states[0] if (state[0] >= 117) and (index is not None) ]
cdrRegion = []
next = 105
for si in range( cys_si+1, jRegion[0][1] ):
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