bioaln: slice-orfs: set orf slice names flat

wqiu · wqiu · commit 4ef187c6bf48 · 2025-08-01T04:00:17.000-04:00
diff --git a/lib/Bio/BPWrapper/AlnManipulations.pm b/lib/Bio/BPWrapper/AlnManipulations.pm
@@ -857,6 +857,7 @@ sub orf_slice {    # get alignment slice
 
 	# remove stop codon
 	$slice = $slice->slice(1, $slice->length() - 3);
+	$slice->set_displayname_flat();
 	my $out = Bio::AlignIO -> new(-file => ">$fname", -format => "fasta");
 	$out->write_aln($slice);
     }

Original file line number	Diff line number	Diff line change
`@@ -857,6 +857,7 @@ sub orf_slice { # get alignment slice`
`857`	`857`
`858`	`858`	`# remove stop codon`
`859`	`859`	`$slice = $slice->slice(1, $slice->length() - 3);`
	`860`	`+ $slice->set_displayname_flat();`
`860`	`861`	`my $out = Bio::AlignIO -> new(-file => ">$fname", -format => "fasta");`
`861`	`862`	`$out->write_aln($slice);`
`862`	`863`	`}`