Commit 271bc8db authored by Sebastien Moretti's avatar Sebastien Moretti
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parent 6606ade4
......@@ -1060,10 +1060,12 @@ sub runExonerate{
# Warning: Arbitrarily threshold between genomic and transcript sequence lengths, fixed at 5000 bp here
# To manage short DNA seq, everything pass through --model protein2genome but with --exhaustive for short ones
if ( -s "$cache/$gis[$b].fas" > 5000 ){
system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError"); #Exonerate prot - genomic or long RNA
# Exonerate prot - genomic or long RNA
system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError");
}
else{
system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 --exhaustive -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError"); #Exonerate prot - short genomic or RNA
# Exonerate prot - short genomic or short RNA
system("$exonerate_exe --showquerygff --showtargetgff --model protein2genome --bestn 1 --percent 75 --exhaustive -q $cache/$date.$order.fas -t $cache/$gis[$b].fas >$cache/$date.$order.exon 2>>$cache/$date.ExonerateError");
}
my $targetNT = $gis[$b];
......@@ -1071,17 +1073,18 @@ sub runExonerate{
print "\n@@ -> $b ... $targetNT\n" if ( $debug );
unlink("$cache/Error:") if ( $tmp == 0 || -z "$cache/Error:" ); #Remove exonerate Error file is it fails to align protein and nucleotide sequences
# Remove exonerate Error file is it fails to align protein and nucleotide sequences
unlink("$cache/Error:") if ( $tmp == 0 || -z "$cache/Error:" );
if ( !-e "$cache/$date.$order.exon" || (-s "$cache/$date.$order.exon") < 520 ){
if ( !-e "$cache/$date.$order.exon" || -s "$cache/$date.$order.exon" < 520 ){
print "\tProtein-Nucleotide alignment has FAILED for $targetNT with $fasta_header\n";
next RUN_EXONERATE;
}
print "\tProtein-Nucleotide alignment was successful for $targetNT with $fasta_header\n";
#Parse Exonerate output
# Parse Exonerate output
my ($posiTions, $posBOJ) = Exonerate::parser("$cache/$date.$order.exon", $debug);
......
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