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Type confusion with get_lineage - tax_id can be int, or str #8

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Type confusion with get_lineage - tax_id can be int, or str#8
#9
@jakobnissen

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@jakobnissen
jakobnissen
opened on May 19, 2025

In get_lineage, the types are not specified, and tax_id can be of either int or str. Indeed, the function itself seems confused as to what they are, with both the check tax_id == 1 and the check tax_id != '1'.

taxconverter/taxconverter/__main__.py

Lines 75 to 89 in 9050fef

def get_lineage(tax_id, map_child_parent):
if tax_id == 0 or tax_id == 1:
logger.info(f"No lineage for ID: {tax_id}")
return ''
if tax_id not in map_child_parent:
logger.info(f"ID not found in NCBI lineage: {tax_id}")
return ''
lineage = []
while tax_id in map_child_parent and tax_id != '1':
lineage.append(tax_id)
tax_id = map_child_parent[tax_id]
if tax_id != '1':
logger.info(f"Parent node warning: {tax_id} is the root, but does not stem from 1. Returning empty lineage.")
return ''
return ';'.join(lineage[::-1])

This causes bugs in a trial run of Taxonverter.

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