diff mutspecSplit.pl @ 0:8c682b3a7c5b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mutspecSplit.pl	Tue Apr 19 03:07:11 2016 -0400
@@ -0,0 +1,64 @@
+# !/usr/bin/perl
+
+#-----------------------------------#
+# Author: Vincent                   #
+# Script: mutspecSplit.pl           #
+# Last update: 01/07/14             #
+#-----------------------------------#
+
+
+use strict;
+use warnings;
+use Getopt::Long;
+
+our $file="";
+our $column="";
+our $path="";
+our $key="";
+
+
+GetOptions('file|f=s'		=>\$file,
+		   'key|k=s'      	=>\$key,
+		   'column|i=s'		=>\$column,
+		   'path|p=s'     	=>\$path);
+
+
+mkdir ("outputFiles") or die ("Erreur creation repertoire\n");
+# print $file,"\n", $key,"\n", $column,"\n", $path,"\n"; exit;
+
+my %tab;
+if ($column==0) {$column++;}
+$column--;
+
+open(FILE, "$file") or die "cannot open $file\n";
+
+$_=<FILE>; #skip headers
+chomp;
+my @line = split(/\t/,$_);
+my $headers = join("\t", @line[0..($column-1),($column+1)..$#line]);
+
+while(<FILE>){
+	chomp;
+	my @line = split(/\t/,$_);
+	#if (!exists($tab{$line[$column]})) { $tab{$line[$column]}=[]; }
+	#push( @{ $tab{$line[$column]} }, join("\t", @line[0..($column-1),($column+1)..$#line]) );
+	my $tmp = join("\t", @line[0..($column-1),($column+1)..$#line]) ;
+	my $id = $line[$column];
+	push( @{ $tab{$id} }, $tmp);
+}
+
+
+while( my ($name,$lines) = each(%tab) ) {
+	my $output="outputFiles/$name";
+	#my $output="primary_$key" . "_$name" . "_visible_tabular";
+	# my $output=$name;
+	open(FILE, ">$output") or die "cannot create file $output \n";
+	print FILE $headers."\n";
+	foreach my $line (@{$lines}){
+		print FILE "$line\n";
+	}
+	close FILE;
+}
+
+my $list=`ls outputFiles/*`;
+print ($list);