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fix(gtdb-parser): respect --use_ncbi_taxonomy in novel-species filter #13

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Merged
thanhleviet merged 1 commit into from
May 19, 2026
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fix(gtdb-parser): respect --use_ncbi_taxonomy in novel-species filter #13

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8 changes: 6 additions & 2 deletions gambitdb/GtdbSpreadsheetParser.py
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@Michal-Babins Michal-Babins May 19, 2026

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Makes sense. LGTM

Original file line number Diff line number Diff line change
Expand Up @@ -156,10 +156,14 @@ def filter_input_spreadsheet(self, input_spreadsheet_df):
input_spreadsheet_df = input_spreadsheet_df[input_spreadsheet_df['contig_count'] <= self.max_contigs]
self.stats_contig_count = len(input_spreadsheet_df.index)

# filter spreadsheet so that if the gtdb_taxonomy column ends with ' sp' followed by digits, then remove the row
# filter spreadsheet so that if the species column ends with ' sp' followed by digits, then remove the row
# These are novel species that GTDB has made up that dont exist in NCBI.
# We check 'species' (not 'gtdb_taxonomy') so that --use_ncbi_taxonomy is honoured: once
# the species column has been rewritten to NCBI names, placeholder GTDB clades (e.g.
# "ECMA0423 sp047199055") will no longer match and genuine NCBI species (e.g. "Shigella
# flexneri") won't be incorrectly dropped.
if not self.include_novel_species:
input_spreadsheet_df = input_spreadsheet_df[~input_spreadsheet_df['gtdb_taxonomy'].str.contains(r' sp\d+$')]
input_spreadsheet_df = input_spreadsheet_df[~input_spreadsheet_df['species'].str.contains(r' sp\d+$', na=False)]
self.stats_include_novel_species = len(input_spreadsheet_df.index)

# if include_derived_samples is False then only include rows with 'none' from ncbi_genome_category
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