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#!/usr/bin/perl
#
# summarize multiple identical hints to one with mult=n
#
# Mario Stanke, 4.1.2010
use strict;
use Getopt::Long;
my $usage = "$0 -- summarize multiple identical hints to one with mult=n\n";
$usage .= "\n";
$usage .= "Usage: $0 <in.psl >joined.psl\n";
$usage .= " PREREQUISITE: input GFF file must be sorted so that hints that should be summarized are below each other\n";
$usage .= " e.g. do a cat hints.gff | sort -n -k 4,4 | sort -s -n -k 5,5 | sort -s -k 3,3 | sort -s -k 1,1 | join_mult_hints.pl\n";
my $help=0;
GetOptions('help!'=>\$help);
if ($help) {
print "$usage";
exit(0);
}
my @f;
my @lf;
my ($lm,$m);
while (<>) {
@f = split(/\t/,$_);
if (!(@lf)){
@lf = @f;
} elsif (!(($f[0] eq $lf[0]) && ($f[2] eq $lf[2]) && ($f[3] == $lf[3]) && ($f[4] == $lf[4]) && ($f[6] eq $lf[6]) && ($f[7] eq $lf[7]))){
print join("\t",@lf);
@lf = @f;
} else {
# update lf by adding f to it
$lf[8] =~ s/gro?u?p=[^;]*;//;
if ($lf[8] =~ /mult=(\d+);/){
$lm = $1;
$lf[8] =~ s/mult=\d+;//;
} else {
$lm = 1;
}
if ($f[8] =~ /mult=(\d+);/){
$m = $1;
} else {
$m = 1;
}
$lf[8] = "mult=" . ($lm+$m) . ";" . $lf[8];
}
}
print join("\t",@lf) if (@lf);
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