Hi there fellow mongers, I am working on a clustering process. I have to parse a file on basis if relativeness. So basically in terms of a example what I want to do is

Input file :example.txt

Gene1,Gene2,spc1,spc2
Gene3,Gene1,spc1,spc2,spc4
Gene4,Gene1,spc1,spc2,spc5,spc3,spc1
Gene2,Gene3,spc1,spc2
Gene2,Gene4,spc2,spc3
Gene3,Gene4,spc1,spc2
GeneA,GeneB,spc4,spc5
GeneB,GeneC,spc1,spc2
GeneC,GeneD,spc1,spc2
GeneD,GeneE,spc4,spc2
GeneE,GeneF,spc3,spc1
GeneX,GeneY,spc6,spc8
GeneX,GeneP,spc6,spc7

My desired Output is
Gene1,Gene2,Gene3,Gene4,spc1,spc2,spc1,spc2,spc4,spc1,spc2,spc5,spc1,spc2,spc2,spc3,spc1,spc2
GeneA,GeneB,GeneC,GeneD,GeneE,GeneF,spc4,spc5,spc1,spc2,spc1,spc2,spc4,spc2,spc3,spc1
GeneX,GeneY,GeneP,,spc6,spc8,spc6,spc7


Currently I am working only on the first half problem .All I am trying to do is get the Gene"X" to cluster.



#!/usr/bin/perl
use strict;
use warnings;

my $file = $ARGV[0];
my %GFs = get_gene_families($file);
foreach my $key (keys(%GFs)){
print $key.$GFs{$key}."\n";
}
exit;

sub get_gene_families{
my $fileName = $_[0];
my %hash = ();
open(IFILE, "$fileName") or die "Couldn't open: $fileName\n";
while(my $line = <IFILE>){
my @genes = split(/\,/, $line);
my $new = 1;
foreach my $key (keys(%hash)){
my @split = split(/\,/, $hash{$key});
push(@split, $key);
if(contains($genes[0], \@split) && contains($genes[1], \@split)){
$new = 0;
}
if(contains($genes[0], \@split) && !contains($genes[1], \@split)){
$hash{$key} .= ",".$genes[1];
$new = 0;
}
if(!contains($genes[0], \@split) && contains($genes[1], \@split)){
$hash{$key} .= ",".$genes[0];
$new = 0;
}
}
if($new){
$hash{$genes[0]} .= ",".$genes[1];
}
}
close IFILE;
return %hash;
}

sub contains{
my $target = $_[0];
my @array = @{$_[1]};
foreach my $element (@array){
if($element eq $target){
return 1;
}
else
}
return 0;
}

[download]
But the output I am getting is

Gene1,Gene2,Gene3,Gene4
GeneB,GeneC
Gene2,Gene3,Gene4
GeneE,GeneF
GeneD,GeneE

,
GeneC,GeneD
GeneA,GeneB
Gene3,Gene4
GeneX,GeneY,GeneP



CAN ANY BODY PLEASE HELP I have been stuck with this problem for a over two weeks now. And I have not yet managed to deal with the first half of the problem.

In reply to Clustering with Perl by nerve

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