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ValueError: invalid literal for int() with base 10: '1.7e+07' #252

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sigven opened this issue Oct 7, 2024 · 0 comments
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ValueError: invalid literal for int() with base 10: '1.7e+07' #252

sigven opened this issue Oct 7, 2024 · 0 comments
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@sigven
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sigven commented Oct 7, 2024

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'
@sigven sigven self-assigned this Oct 7, 2024
@sigven sigven closed this as completed Oct 29, 2024
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