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speedup and cleanup
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Michael Paulini committed Oct 26, 2018
1 parent 9e5b26b commit ee370b0
Showing 1 changed file with 7 additions and 5 deletions.
12 changes: 7 additions & 5 deletions scripts/confirm_genes.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -623,14 +623,16 @@ sub create_transcript_file {
}else {
$prefix = $wormbase->chromosome_prefix."${chrom}_";
}
my $trinity = -e "${gffdir}/${prefix}BLAT_Trinity_BEST.gff" ? "${prefix}BLAT_Trinity_BEST.gff" : '';
my $isoseq = -e "${gffdir}/${prefix}BLAT_IsoSeq_BEST.gff" ? "${prefix}BLAT_IsoSeq_BEST.gff" : '';

$wormbase->run_command("cd $gffdir; cat ${prefix}BLAT_EST_BEST.gff ${prefix}BLAT_mRNA_BEST.gff $trinity $isoseq > ${prefix}BLAT_TRANSCRIPT_BEST.gff", $log);
my $file = "${prefix}BLAT_TRANSCRIPT_BEST.gff";

return if $file; # don't rebuild the file every single time

# only elegans has OSTs and RSTs
$wormbase->run_command("cd $gffdir; cat ${prefix}BLAT_OST_BEST.gff ${prefix}BLAT_RST_BEST.gff >> ${prefix}BLAT_TRANSCRIPT_BEST.gff", $log) if ($wormbase->species eq 'elegans');
my $trinity = -e "${gffdir}/${prefix}BLAT_Trinity_BEST.gff" ? "${prefix}BLAT_Trinity_BEST.gff" : '';
my $isoseq = -e "${gffdir}/${prefix}BLAT_IsoSeq_BEST.gff" ? "${prefix}BLAT_IsoSeq_BEST.gff" : '';
my $more = ($wormbase->species eq 'elegans') ? "${prefix}BLAT_OST_BEST.gff ${prefix}BLAT_RST_BEST.gff" : ''; # only elegans has OSTs and RSTs

$wormbase->run_command("cd $gffdir; cat ${prefix}BLAT_EST_BEST.gff ${prefix}BLAT_mRNA_BEST.gff $trinity $isoseq $more > $file", $log);
}
################

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