fix(gtdb-parser): respect --use_ncbi_taxonomy in novel-species filter#13
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thanhleviet merged 1 commit intoMay 19, 2026
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The novel-species filter read the raw gtdb_taxonomy column while --use_ncbi_taxonomy rewrites only the species column. This caused genomes with NCBI-named species but GTDB placeholder taxonomy (e.g. NCBI Shigella flexneri / GTDB s__ECMA0423 sp047199055) to be dropped, ultimately yielding zero S. flexneri in the Escherichia/Shigella build. Switch the filter to read the species column so it sees post-rewrite names. Add na=False to tolerate rows missing a species call, which the species column (unlike gtdb_taxonomy) does not guarantee to populate.
Michal-Babins
approved these changes
May 19, 2026
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Summary
The novel-species filter at
GtdbSpreadsheetParser.py:166was reading the rawgtdb_taxonomycolumn to drop GTDB placeholder species (sp###), but--use_ncbi_taxonomyand--ncbi_whitelistonly rewrite the derivedspeciescolumn. As a result, genomes whose NCBI name is a real species but whose GTDB name is a placeholder were silently dropped — most visibly losing 797 of 837 Shigella flexneri rows and yielding zero S. flexneri in the final Escherichia/Shigella database.This PR points the filter at the
speciescolumn instead. Default builds are unaffected because both columns hold the same value when no rename flag is set. Builds with--use_ncbi_taxonomyor--ncbi_whitelistnow correctly preserve NCBI-named species. Addedna=Falseso blank cells in thespeciescolumn don't raise during the regex check.Changes
gambitdb/GtdbSpreadsheetParser.py:166— switch column fromgtdb_taxonomytospecies; addna=False.Test plan
GtdbSpreadsheetParserunit tests pass (2/2 green); 10 unrelated pre-existing failures in the wider suite are present on unmodified main and not caused by this change.--use_ncbi_taxonomy: Shigella flexneri now appears withngenomes=6(was 0 before fix).--use_ncbi_taxonomy: genuinesp\d+$placeholders still correctly dropped (regression check).ngenomesinspecies_taxa.csvfor the affected species.--use_ncbi_taxonomyor--ncbi_whitelist— the same rows are dropped becausespeciesis derived fromgtdb_taxonomyin that path.Out of scope
A secondary issue exists where species whose accessions are removed by the minimum-genomes filter still appear in
species_taxa.csvwith emptyngenomes(lines 202-235). This is independent of the column-mismatch bug fixed here and can fire under any flag combination. To be addressed in a follow-up.