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#!/usr/bin/perl
#
# convert the retroGenes track to a file with hints to AUGUSTUS
#
use strict;
use Getopt::Long;
my ($usage, $priority, $grp);
my ($chrom, $name, $chromStart, $blockCount, $blockSizes, $chromStarts, $score);
my $source = 'R';
my $max_small_gap_len = 30;
my $minscore=650;
#default values
$priority = 4;
$usage .= "$0 -- convert retroposed genes output to hints\n";
$usage .= "Usage: $0 [--priority=p --minscore=a --maxSmallGapLen=m --source=s]\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";
$usage .= "echo \"select name, chrom, strand, cdsStart, cdsEnd from exoniphy order by chrom, cdsStart;\" | hgsql hg18 | grep -v cdsStart\n";
GetOptions('priority:i'=>\$priority,
'source:s' =>\$source,
'minscore:i' =>\$minscore,
'maxSmallGapLen:i'=>\$max_small_gap_len);
my ($from, $to, $newfrom, $newto);
while (<>) {
chomp;
my @f = split /\t/, $_;
next unless (@f > 6);
$chrom = $f[0];
$name = $f[1];
$score = $f[2];
$chromStart = $f[3];
$blockCount = $f[4];
$blockSizes = $f[5];
$chromStarts = $f[6];
next unless ($score >= $minscore);
my @sizes = split /,/, $blockSizes;
my @starts = split /,/, $chromStarts;
$from = $to = -1000;
for (my $i=0; $i<$blockCount; $i++) {
$newfrom = $chromStart + $starts[$i] + 1;
$newto = $chromStart + $starts[$i] + 1 + $sizes[$i]-1;
if ($to >= 0 && $to < $newfrom - $max_small_gap_len - 1) {
print "$chrom\tretro\tnonexonpart\t$from\t$to\t$score\t\.\t.\tgrp=$name:$chromStart;src=$source;pri=$priority\n";
$from = $newfrom;
} elsif ($from<0) {
$from = $newfrom;
}
$to = $newto;
}
print "$chrom\tretro\tnonexonpart\t$from\t$to\t$score\t\.\t.\tgrp=$name:$chromStart;src=$source;pri=$priority\n";
}
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