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tgr2tg
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tgr2tg
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#!/usr/bin/perl
use warnings;
use strict;
use fralib;
use Getopt::Long;
use Pod::Usage;
use File::Basename;
use Switch;
=head1 NAME
tgr2tg
=head1 SYNOPSIS
tgr2tg [options] tgr-file
-m marker annotation file
a)snp-id
b)alleles
tg-file tg file
example: tgr2tg -m pscalare.mk pscalare.tg
Converts tgr file to tgr format.
=head1 DESCRIPTION
=cut
#option variables
my $help;
my $mkFile;
my $tgrFile;
my $tgFile;
my %MARKER;
my $colNo;
my %label2Column;
my $headerProcessed;
#initialize options
Getopt::Long::Configure ('bundling');
if(!GetOptions ('h'=>\$help, 'm=s'=>\$mkFile)
|| !defined($mkFile)
|| scalar(@ARGV)!=1)
{
if ($help)
{
pod2usage(-verbose => 2);
}
else
{
pod2usage(1);
}
}
open(MK, $mkFile) || die "Cannot open $mkFile";
$headerProcessed = 0;
while(<MK>)
{
s/\r?\n?$//;
if(!$headerProcessed)
{
$colNo = s/\t/\t/g + 1;
my @fields = split('\t', $_, $colNo);
SEARCH_LABEL: for my $label ('marker_id', 'alleles')
{
for my $col (0 .. $#fields)
{
if ($fields[$col] eq $label)
{
$label2Column{$label}=$col;
next SEARCH_LABEL;
}
}
die "Cannot find '$label' in $mkFile";
}
$headerProcessed = 1;
}
else
{
my @fields = split('\t', $_, $colNo);
my $marker = $fields[$label2Column{'marker_id'}];
my $alleles = $fields[$label2Column{'alleles'}];
my @alleles = split("/", $alleles);
for my $i (0 .. $#alleles)
{
$MARKER{$marker}{$alleles[$i]} = $i;
}
}
}
close(MK);
$tgrFile = $ARGV[0];
my ($name, $path, $ext) = fileparse($tgrFile, '\..*');
$tgFile = "$name.tg";
open(TGR, "$tgrFile") || die "Cannot open $tgrFile\n";
open(TG, ">$tgFile") || die "Cannot open $tgFile\n";
$headerProcessed = 0;
while (<TGR>)
{
s/\r?\n?$//;
if(!$headerProcessed)
{
#counts number of columns
$colNo = s/\t/\t/g + 1;
my @fields = split('\t', $_, $colNo);
print TG "$_\n";
$headerProcessed = 1;
}
else
{
my @fields = split('\t', $_, $colNo);
my $marker = $fields[0];
if (exists($MARKER{$marker}))
{
print TG "$marker";
for my $col (1..$#fields)
{
my @genotypes = split("/", $fields[$col]);
my $g0 = -1;
my $g1 = -1;
if ($genotypes[0]!=-1)
{
$g0 = $MARKER{$marker}{$genotypes[0]};
}
if ($genotypes[1]!=-1)
{
$g1 = $MARKER{$marker}{$genotypes[1]};
}
print TG "\t$g0/$g1";
}
print TG "\n";
}
else
{
warning("$marker does not exist in $mkFile, ignored");
}
}
}
close(TGR);
close(TG);