diff --git a/lib/python/anarci/anarci.py b/lib/python/anarci/anarci.py index 4069994..e141faa 100644 --- a/lib/python/anarci/anarci.py +++ b/lib/python/anarci/anarci.py @@ -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',''), @@ -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] )