annotate admixture/Admixture.pl @ 12:a03f54c420f1 draft

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#!/usr/bin/perl

use strict;
use Switch;
use Getopt::Long;
use Bio::SeqIO;

my $usage = qq~Usage:$0 <args> [<opts>]
where <args> are:
    -i, --input         <input HAPMAP>
    -o, --output        <output>
    -k, --kmin          <K min. int>
    -m, --maxK          <K max. int>
    -d, --directory     <temporary directory>
    -p, --path          <path to executables>
~;
$usage .= "\n";

my ($input,$output,$kmin,$kmax,$directory,$path);


GetOptions(
	"input=s"      => \$input,
	"output=s"     => \$output,
	"kmin=s"       => \$kmin,
	"maxK=s"       => \$kmax,
	"directory=s"  => \$directory,
	"path=s"       => \$path
);


die $usage
  if ( !$input || !$output || !$kmin || !$kmax || !$directory || !$path);

if ($kmin =~/^(\d+)\s*$/){
        $kmin = $1;
}
else{
        die "Error: kmin must be an integer\n";
}
if ($kmax =~/^(\d+)\s*$/){
        $kmax = $1;
}
else{
        die "Error: kmax must be an integer\n";
}

  
######################
# create map file
######################
open(my $M,">$directory/input.map");
open(my $H,$input);
<$H>;
while(<$H>)
{
	my @infos = split(/\t/,$_);
	print $M $infos[2] . "\t" . $infos[0] . "\t" . "0" . "\t" . $infos[3] . "\n";
}
close($H);
close($M);

######################
# create ped file
######################
system("$path/transpose.awk $input >$directory/input.ped.2");

open(my $P,">$directory/input.ped");
open(my $P2,"$directory/input.ped.2");
my $n = 0;
my $ind_num = 0;
my @individus;
while(<$P2>)
{
	$n++;
	if ($n > 11)
	{
		my $line = $_;
		$line =~s/N/0/g;
		if (/^([^\s]+)\s+(.*)$/)
		{
			$ind_num++;
			my $ind = $1;
			push(@individus,$ind);
			my $genoyping_line = $2;
			print $P "$ind	$ind_num	0	0	1	2";
			my @genotypes = split(/\s/,$genoyping_line);
			foreach my $genotype(@genotypes)
			{
				$genotype =~s/N/0/g;
				my @alleles = split("",$genotype);
				print $P "	" . join(" ",@alleles);
			}
			
			print $P "\n";
		}
	}
}
close($P2);
close($P);

unlink("$directory/input.ped.2");

system("plink --file $directory/input --out $directory/out --make-bed --noweb >>$directory/plink.log 2>&1");


###################################
# launch admixture for different K
###################################
my %errors;
for (my $k = $kmin; $k <= $kmax; $k++)
{
	system("admixture --cv $directory/out.bed $k >>$directory/log.$k 2>&1");
	my $cv_error_line = `grep -h CV $directory/log.$k`;
	if ($cv_error_line =~/: (\d+\.*\d*)$/)
	{
		$errors{$1} = $k;
	}
	system("cat $directory/log.$k >>$directory/logs");
	system("echo '\n\n====================================\n\n' >>$directory/logs");
	system("cat out.$k.Q >>$directory/outputs.Q");
	system("echo '\n\n====================================\n\n' >>$directory/outputs.Q");
	system("cat out.$k.P >>$directory/outputs.P");
	system("echo '\n\n====================================\n\n' >>$directory/outputs.P");
}

my @sorted_errors = sort {$a<=>$b} keys(%errors);
my $best_K = $errors{@sorted_errors[0]};


#system("cp -rf out.$best_K.Q $directory/output");

open(BEST1,"out.$best_K.Q");
open(BEST2,">$directory/output");
print BEST2 "<Covariate>\n";
print BEST2 "<Trait>";
for (my $j=1;$j<=$best_K;$j++)
{
	print BEST2 "	Q" . $j;
}
print BEST2 "\n";
my $i = 0;
while(<BEST1>)
{
	my $line = $_;
	$line =~s/ /\t/g;
	my $ind = $individus[$i];
	print BEST2 "$ind	";
	print BEST2 $line;
	$i++;
}
close(BEST1);
close(BEST2);

system("cp -rf $directory/log.$best_K $directory/log");