diff Admixture.pl @ 4:58df6910f1c3 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Admixture.pl	Tue Apr 12 09:31:56 2016 -0400
@@ -0,0 +1,147 @@
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+use File::Basename;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+where <args> are:
+    -i, --input         <input basename (for PED, FAM, BIM)>
+    -o, --output        <output>
+    -k, --kmin          <K min. int>
+    -m, --maxK          <K max. int>
+    -d, --directory     <temporary directory>
+~;
+$usage .= "\n";
+
+my ($input,$output,$kmin,$kmax,$directory);
+
+
+GetOptions(
+	"input=s"      => \$input,
+	"output=s"     => \$output,
+	"kmin=s"       => \$kmin,
+	"maxK=s"       => \$kmax,
+	"directory=s"  => \$directory,
+);
+
+
+die $usage
+  if ( !$input || !$output || !$kmin || !$kmax || !$directory );
+
+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";
+}
+
+
+
+open(my $P2,"$input.fam");
+my $n = 0;
+my $ind_num = 0;
+my @individus;
+while(<$P2>)
+{
+	my ($ind,$other) = split(/ /,$_);
+	push(@individus,$ind);
+}
+close($P2);
+
+my $basename = basename($input);
+
+###################################
+# launch admixture for different K
+###################################
+my %errors;
+for (my $k = $kmin; $k <= $kmax; $k++)
+{
+	system("admixture --cv $input.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");
+
+	open(my $O2,">$basename.$k.final.Q");
+	open(my $O,"$basename.$k.Q");
+	my %hash_groupes;
+	my %hash_indv;
+	my %group_of_ind;
+	my $i = 0;
+	while (<$O>){
+		$i++;
+		my $line = $_;
+		$line =~s/\n//g;
+		$line =~s/\r//g;
+		my @infos = split(/\s+/,$line);
+		my $group = "admix";
+		my $ind = $individus[$i];
+		for (my $j = 0; $j <$k; $j++){
+			my $val = $infos[$j];
+			if ($val > 0.5){$group = "Q$j";}
+		}
+		if ($ind){      
+			$hash_indv{$ind} = join("	",@infos);
+			$hash_groupes{$group}{"ind"} .= ",".$ind;
+			$group_of_ind{$ind} = $group;
+		}
+	}
+	close($O);
+
+	foreach my $group(sort keys(%hash_groupes)){
+		my @inds = split(",",$hash_groupes{$group}{"ind"});
+		foreach my $ind(@inds){
+			if ($ind =~/\w+/){
+				#print $O3 "$ind;$group\n";
+				print $O2 $ind."	".$hash_indv{$ind}. "\n";
+			}
+		}
+	}
+	#close($O3);
+	close($O2);
+
+	system("cat $basename.$k.final.Q >>$directory/outputs.Q");
+	system("echo '\n\n====================================\n\n' >>$directory/outputs.Q");
+	system("cat $basename.$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 = $errors{@sorted_errors[0]};
+
+
+open(BEST1,"$basename.$best_K.final.Q");
+open(BEST2,">$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;
+	print BEST2 $line;
+	$i++;
+}
+close(BEST1);
+close(BEST2);
+
+system("cp -rf $directory/log.$best_K $directory/log");
+
+
+
+