ValueError: invalid literal for int() with base 10: '1.7e+07' #252
Description
in pcgr_summarise, there is a bug for one (or more) selected transcripts in the calculation of distance to coding sequence start, given the scientific encoding of the coding sequence start (1.7e+07) that is not properly handled during conversion to integer.
Version of PCGR: 2.1.0
Genome build: grch37
Full error message:
Traceback (most recent call last):
File "/Users/sigven/project_data/packages/package__pcgr/installation2/pcgr/bin/pcgr_summarise.py", line 281, in <module>
__main__()
File "/Users/sigven/project_data/packages/package__pcgr/installation2/pcgr/bin/pcgr_summarise.py", line 46, in __main__
extend_vcf_annotations(arg_dict, logger)
File "/Users/sigven/project_data/packages/package__pcgr/installation2/pcgr/bin/pcgr_summarise.py", line 198, in extend_vcf_annotations
parse_vep_csq(rec, transcript_xref_map, vep_csq_fields_map, arg_dict['vep_pick_order'],
File "/Users/sigven/project_data/packages/package__pcgr/pcgr/pcgr/vep.py", line 358, in parse_vep_csq
csq_record = get_csq_record_annotations(csq_fields, varkey, logger, vep_csq_fields_map, transcript_xref_map)
File "/Users/sigven/project_data/packages/package__pcgr/pcgr/pcgr/vep.py", line 148, in get_csq_record_annotations
csq_record = assign_cds_exon_intron_annotations(csq_record, logger)
File "/Users/sigven/project_data/packages/package__pcgr/pcgr/pcgr/annoutils.py", line 404, in assign_cds_exon_intron_annotations
csq_record['CDS_DISTANCE'] = abs(int(csq_record['CDS_START']) - int(csq_record['VARKEY'].split('_')[1]))
ValueError: invalid literal for int() with base 10: '1.7e+07'
Metadata
Metadata
Assignees
Labels
No labels