mutspecSplit.pl

# !/usr/bin/perl

#-----------------------------------#
# Author: Vincent                   #
# Script: mutspecSplit.pl           #
# Last update: 24/02/17             #
#-----------------------------------#


use strict;
use warnings;
use Getopt::Long;

our $file="";
our $column="";
our $path="";
our $key="";
our $help=0;


GetOptions('file|f=s'		=>\$file,
		       'column|i=s'	=>\$column,
		       'help|h'     =>\$help) or do_help(); # 'key|k=s'      	=>\$key,

if($help)
{
	do_help();
}

if ( ($file eq "") || ($column eq "") )
{
	do_help();
}

sub do_help
{
	print "Usage: mutspecSplit.pl --file <input_file> --column <value>\n
	Option --file: Input file to split\n
	Option --column: Column number containing the samples ids (start to count from 1)\n\n";
	exit;
}


mkdir ("outputFiles") or die ("Erreur creation repertoire\n");
# print $file,"\n", $key,"\n", $column,"\n", $path,"\n"; exit;

my %tab;
if ($column==0) {$column++;} # Start to count from 1
$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);