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Fix error when j_gene is None #83

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Fix error when j_gene is None #83

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10 changes: 8 additions & 2 deletions lib/python/anarci/anarci.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,6 +273,12 @@ def csv_output(sequences, numbered, details, outfileroot):

# Iterate over the domains identified
for i,j in chain_types[cts]:
try:
j_gene_name = details[i][j].get('germlines',{}).get( 'j_gene',[['',''],0] )[0][1]
j_gene_identity = '%.2f'%details[i][j].get('germlines',{}).get( 'j_gene',[['',''],0] )[1]
except TypeError:
j_gene_name = None
j_gene_identity = 0
line = [ sequences[i][0].replace(',',' '),
str(j),
details[i][j].get('species',''),
Expand All @@ -284,8 +290,8 @@ def csv_output(sequences, numbered, details, outfileroot):
details[i][j].get('germlines',{}).get( 'v_gene',[['',''],0] )[0][0],
details[i][j].get('germlines',{}).get( 'v_gene',[['',''],0] )[0][1],
'%.2f'%details[i][j].get('germlines',{}).get( 'v_gene',[['',''],0] )[1],
details[i][j].get('germlines',{}).get( 'j_gene',[['',''],0] )[0][1],
'%.2f'%details[i][j].get('germlines',{}).get( 'j_gene',[['',''],0] )[1] ]
j_gene_name,
j_gene_identity ]

# Hash the numbering. Insertion order has been preserved in the positions sort.
d = dict( numbered[i][j][0] )
Expand Down