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bug-fix: stop codons not registered when parsing alignments for metap… #274

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bug-fix: stop codons not registered when parsing alignments for metap… #274

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bug-fix: stop codons not registered when parsing alignments for metap…
thepatientwait Dec 12, 2025
9ea58ce
removed old TODO comment
thepatientwait Dec 12, 2025
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1 change: 0 additions & 1 deletion singlem/diamond_spkg_searcher.py
100644 → 100755
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Expand Up @@ -106,7 +106,6 @@ def _prefilter(self, diamond_database, read_files, is_reverse_reads, performance

# creating new read index to account for multiple hits
# by concating the read_name with the marker_gene_name, we can ensure only 1 gene copy per read
# TODO: add an option to let all unique genes through with range-uclling
qseqid = qseqid + '••' + sseqid.split('~')[0]

# extra check to make sure we're not overwriting a better hit
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2 changes: 1 addition & 1 deletion singlem/metagenome_otu_finder.py
100644 → 100755
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Expand Up @@ -90,7 +90,7 @@ def find_windowed_sequences(self,

def _find_lower_case_columns(self, protein_alignment):
lower_cases = [False]*len(protein_alignment[0].seq)
lower_case_chars = re.compile(r'[a-z]')
lower_case_chars = re.compile(r'[a-z\*]')
for pro in protein_alignment:
for i, aa in enumerate(pro.seq):
if lower_case_chars.match(aa):
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