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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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Add stop lost variants to hgvs parsing #358

Closed jodyphelan closed 1 month ago

jodyphelan commented 1 month ago

Database create function currently fails with p.Ter187Argext*? variant. Need to add parser to HGVS module.

Error:

Don't know how to handle {'name': 'pncA', 'gene_id': 'Rv2043c', 'strand': '-', 'chrom': 'NC_000962.3', 'feature_start': 2288681, 'feature_end': 2289241, 'start': 2289241, 'end': 2288681, 'length': 561, 'transcripts': [<pathogenprofiler.gff.Transcript object at 0x7fbb200007d0>]} p.*187Arg