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get_LOD_peak.pl(MapQTL6.0)

已有 2692 次阅读 2017-3-9 15:19 |系统分类:科研笔记

#!/usr/bin/perl -w

#===============================================================

# This script is used to extract the LOD value of a batch of files at 95% informative interval for MapQTL

# By chencheng hengbenxianfeng@163.com

# Start time: 2017/3/6 19:40

# End time: 2017/3/6 20:10

# Title get_LOD_peak.pl

# ===============================================================

use strict;

use File::Basename;

use FindBin qw($Bin);

die "perl $0 <out file>\n" unless @ARGV == 1;

open OUT, ">$ARGV[0]";

print OUT join("\t","Trait","LOD","p_value" ),"\n";

my @file = glob "*mqo";

foreach my $one(@file)

{

open IN, $one || die "cannot open the file\n";

my $count;

my $name = $one;

$name =~ s/Session\ \d\ \(PT\)_HR_bin_geno_//g;

$name =~ s/\.mqo//g;

while(<IN>)

{

chomp;

my @arr = split;

if($arr[1] eq 'GW' and $arr[6] >= 0.945)

{

$count ++;

if($count ==1 )

{

print OUT join ("\t",$name,@arr[2,6]),"n";

}

}

}

close IN;

}

close OUT;




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