bioaln:slice-orfs: remove stop

wqiu · wqiu · commit ef13519c70d2 · 2025-07-31T23:33:49.000-04:00
diff --git a/lib/Bio/BPWrapper/AlnManipulations.pm b/lib/Bio/BPWrapper/AlnManipulations.pm
@@ -854,6 +854,9 @@ sub orf_slice {    # get alignment slice
 	    }
 	    $slice = $new_slice;
 	}
+
+	# remove stop codon
+	$slice = $slice->slice(1, $slice->length() - 3);
 	my $out = Bio::AlignIO -> new(-file => ">$fname", -format => "fasta");
 	$out->write_aln($slice);
     }

Original file line number	Diff line number	Diff line change
`@@ -854,6 +854,9 @@ sub orf_slice { # get alignment slice`
`854`	`854`	`}`
`855`	`855`	`$slice = $new_slice;`
`856`	`856`	`}`
	`857`	`+`
	`858`	`+ # remove stop codon`
	`859`	`+ $slice = $slice->slice(1, $slice->length() - 3);`
`857`	`860`	`my $out = Bio::AlignIO -> new(-file => ">$fname", -format => "fasta");`
`858`	`861`	`$out->write_aln($slice);`
`859`	`862`	`}`