From d53d93ffd943392217502c66f1ef4c0dc6a3f03a Mon Sep 17 00:00:00 2001 From: thepatientwait Date: Fri, 12 Dec 2025 10:25:09 +1000 Subject: [PATCH 1/2] bug-fix: stop codons not registered when parsing alignments for metapackage creation --- singlem/metagenome_otu_finder.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) mode change 100644 => 100755 singlem/metagenome_otu_finder.py diff --git a/singlem/metagenome_otu_finder.py b/singlem/metagenome_otu_finder.py old mode 100644 new mode 100755 index 718b1937..a33680c4 --- a/singlem/metagenome_otu_finder.py +++ b/singlem/metagenome_otu_finder.py @@ -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): From 9ea58ce45f8cf6902a28babe93850a7348229f50 Mon Sep 17 00:00:00 2001 From: thepatientwait Date: Fri, 12 Dec 2025 10:29:21 +1000 Subject: [PATCH 2/2] removed old TODO comment --- singlem/diamond_spkg_searcher.py | 1 - 1 file changed, 1 deletion(-) mode change 100644 => 100755 singlem/diamond_spkg_searcher.py diff --git a/singlem/diamond_spkg_searcher.py b/singlem/diamond_spkg_searcher.py old mode 100644 new mode 100755 index 37fb8d74..4f7515ed --- a/singlem/diamond_spkg_searcher.py +++ b/singlem/diamond_spkg_searcher.py @@ -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