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#!/usr/bin/perl
#
# generate hints from an Exonerate gff dump
# Mario Stanke June, 2007
use strict;
use Getopt::Long;
my $usage = "$0 -- convert exonerate output file to hints file for AUGUSTUS\n";
$usage .= "\n";
$usage .= "Usage: $0 --in=exfile --out=hintsfile\n";
$usage .= " Exonerate run like this: exonerate --model protein2genome --showtargetgff T ... > exfile\n";
$usage .= " options:\n";
$usage .= " --priority=n priority of hint group (default 4)\n";
$usage .= " --minintronlen=n alignments with gaps shorter than this and longer than maxgaplen are discarded (default 41)\n";
$usage .= " --maxintronlen=n alignments with longer gaps are discarded (default 350000\n";
$usage .= " --CDSpart_cutoff=n this many bp are cut off of each CDSpart hint w.r.t. the exonerate cds (default 9)\n";
$usage .= " --source=s source identifier (default 'P')\n";
#$usage .= " --ssOn include splice site (dss, ass) hints in output (default false)\n";
my $exfile;
my $hintsfilename;
my $minintronlen = 41;
my $maxintronlen = 350000;
my $CDSpart_cutoff = 15;
my $source="XNT";
my $priority = 4;
my $prgsrc = "xnt2h";
my $line=0;
my $coloffset=0;
my $ssOn=0;
my $CDSpartid = "CDSpart"; # abbreviate to decrease file size
my $prot="";
if ($#ARGV < 1 ) {
print "$usage";
exit;
}
GetOptions(
'in=s'=>\$exfile,
'out=s'=>\$hintsfilename,
'minintronlen:i'=>\$minintronlen,
'maxintronlen:i'=>\$maxintronlen,
'CDSpart_cutoff:i'=>\$CDSpart_cutoff,
'source:s'=>\$source,
'priority:i'=>\$priority,
'ssOn!'=>\$ssOn);
open(XNT, "<$exfile") || die "Couldn't open $exfile\n";
open(HINTS, ">$hintsfilename") || die "Could not open $hintsfilename";
while (<XNT>) {
s/#.*//;
next unless /\S/;
next unless /\texonerate:protein2genome:local\t/; # modified by Katharina on September 8th 2010 because exonerate output format apparently changed regarding the string "local".q
# print "I am in the file!\n";
my @f = split /\t/, $_, 9;
if (@f < 8) { warn "Not gff format"; next }
my $seqname = $f[0];
my $type = $f[2];
my $start = $f[3];
my $end = $f[4];
my $score = $f[5];
my $strand = $f[6];
# if ($strand eq '-') {
# $start++; # exonerate has a weird coordinate system
# $end++;
# } # apparently this has changed with exonerate versions and it is now standard
if ($end < $start) {
my $tmp = $start;
$start = $end;
$end = $tmp;
}
if ($type eq "intron") {
# length in range?
if ($end - $start + 1 >= $minintronlen && $end - $start + 1 <= $maxintronlen){
print HINTS "$seqname\t$prgsrc\tintron\t$start\t$end\t$score\t$strand\t.\tsrc=$source;grp=$prot;pri=$priority\n";
}
} elsif ($type eq "cds") {
$start += $CDSpart_cutoff;
$end -= $CDSpart_cutoff;
if ($start > $end) {
$start = $end = int(($start+$end)/2);
}
print HINTS "$seqname\t$prgsrc\t$CDSpartid\t$start\t$end\t$score\t$strand\t.\tsrc=$source;grp=$prot;pri=$priority\n";
} elsif ($type eq "gene") {
/sequence (\S+) ; /;
$prot = $1;
}
}
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