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preserve contig names with --centre/--compliant #132

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preserve contig names with --centre/--compliant #132

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13 changes: 10 additions & 3 deletions bin/prokka
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Original file line number Diff line number Diff line change
Expand Up @@ -422,9 +422,16 @@ while (my $seq = $fin->next_seq) {
}
$ncontig++;
# http://www.ncbi.nlm.nih.gov/genomes/static/Annotation_pipeline_README.txt
# leave contigs names as-is unless they are in --compliant mode or want --centre set
if ($centre) {
$seq->id( sprintf "gnl|$centre|${contigprefix}contig%06d", $ncontig );
# leave contig names as-is unless they are in --compliant mode or want --centre set
if ($centre) {
# try to append the original (often shorter than contigXXXXXX) name to $contigprefix even when using --centre/--compliant
if (exists $seq{$seq->id}) {
msg("This contig ID is not unique, and will be replaced with an auto-generated one: ".$seq->id);
$seq->id( sprintf "gnl|$centre|${contigprefix}contig%06d", $ncontig );
}
else {
$seq->id( sprintf "gnl|$centre|${contigprefix}%s", $seq->id );
}
}
if (length($seq->id) > $MAXCONTIGIDLEN) {
msg("Contig ID must <= $MAXCONTIGIDLEN chars long: ".$seq->id);
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