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#!/usr/bin/perl
#
# convert the exoniphy exon predictions to a file with hints to AUGUSTUS
#
use strict;
use Getopt::Long;
my ($usage, $cutoff, $priority, $grp, $seqname, $strand, $begin, $end);
#default values
$cutoff = 9;
$priority = 4;
$usage .= "$0 -- convert exoniphy output to hints file\n";
$usage .= "Usage: $0 [--priority=p --cutoff=c]\n";
$usage .= "reads from stdin writes to stdout.\n";
$usage .= "takes input in tab separated format:\n";
$usage .= "name\tchrom\tstrand\tcdsStart\tcdsEnd\n";
$usage .= "You get this format on the UCSC system by typing e.g.\n";
$usage .= "echo \"select name, chrom, strand, cdsStart, cdsEnd from exoniphy order by chrom, cdsStart;\" | hgsql hg18 | grep -v cdsStart\n";
GetOptions('priority:i'=>\$priority,
'cutoff:i'=>\$cutoff);
while (<>) {
chomp;
my @f = split /\t/, $_;
next unless (@f > 4);
$grp = $f[0];
$seqname = $f[1];
$strand = $f[2];
$begin = $f[3]+1;
$end = $f[4];
print "$seqname\texoniphy\tCDS\t$begin\t$end\t0\t$strand\t.\tgrp=$grp;pri=$priority;src=X\n";
$begin += $cutoff;
$end -= $cutoff;
if ($begin > $end) {
$begin = $end = int(($begin+$end)/2);
}
print "$seqname\texoniphy\tCDSpart\t$begin\t$end\t0\t$strand\t.\tgrp=$grp;pri=$priority;src=X\n";
}
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