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Speed up overlap lookup in CDS stage #493

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Speed up overlap lookup in CDS stage #493

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28 changes: 21 additions & 7 deletions bin/prokka
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Original file line number Diff line number Diff line change
Expand Up @@ -709,6 +709,17 @@ if ($tools{'minced'}->{HAVE}) {
# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
# CDS

# Create a hash of RNA lists, grouped by seqid to speed up lookups.
my %rnabyseq;
for my $rna (@allrna) {
my @a = ();
$rnabyseq{$rna->seq_id} = \@a;
}
for my $rna (@allrna) {
my $a = $rnabyseq{$rna->seq_id};
push @$a, $rna;
}

msg("Predicting coding sequences");
my $totalbp = sum( map { $seq{$_}{DNA}->length } @seq);
my $prodigal_mode = ($totalbp >= 100000 && !$metagenome) ? 'single' : 'meta';
Expand Down Expand Up @@ -744,15 +755,18 @@ while (<$PRODIGAL>) {
}
);
my $overlap;
for my $rna (@allrna) {
# same contig, overlapping (could check same strand too? not sure)
if ($rna->seq_id eq $sid and $cds->overlaps($rna)) {
$overlap = $rna;
last;
}
if (!$cds_rna_olap and exists($rnabyseq{$sid})) {
my $seqrna = $rnabyseq{$sid};
for my $rna (@$seqrna) {
# same contig, overlapping (could check same strand too? not sure)
if ($rna->seq_id eq $sid and $cds->overlaps($rna)) {
$overlap = $rna;
last;
}
}
}
# mitochondria are highly packed, so don't exclude as CDS/tRNA often overlap.
if ($overlap and ! $cds_rna_olap) {
if ($overlap) {
my $type = $overlap->primary_tag;
msg("Excluding CDS which overlaps existing RNA ($type) at $sid:$1..$2 on $3 strand");
}
Expand Down