Re: Clustering with Perl

[Transient]

This is what I used. More of an older style I'd imagine, and probably could be cleaned up a bit, but it works (I think!):

#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

# read in data

my $g_arr = [ ];
my $value_arr = [ ];

while ( <DATA> ) {
  chomp;

  # Assumes 2 genes per line in the first and second position!
  my @line = split /,/, $_, 3; 

  $line[2] =~ s/\s*$//;

  my $cluster_idx = 0;
  my @found = ( -1, -1 );
  foreach my $cluster ( @$g_arr ) {
    foreach my $poss_g_match ( @$cluster ) {
      if ( $line[0] eq $poss_g_match ) {
        $found[0] = 1;
      }
      if ( $line[1] eq $poss_g_match ) {
        $found[1] = 1;
      }
    }
    last if ( $found[0] != -1 || $found[1] != -1 );
    $cluster_idx++;
  }

  if ( $found[0] == -1 ) {
    push @{$g_arr->[$cluster_idx]}, $line[0];
  }
  if ( $found[1] == -1 ) {
    push @{$g_arr->[$cluster_idx]}, $line[1];
  }

  push @{$value_arr->[$cluster_idx]}, $line[2];
}

my $traversal_idx = 0;

foreach my $cluster ( @$g_arr ) {
  print join( ',', @$cluster) . " : " . join( ',', @{$value_arr->[$tra
+versal_idx++]} ), "\n";
}

__DATA__
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
GeneUnknown.,GeneUnknown.,spc1,spc2

Outputs

Gene1,Gene2,Gene3,Gene4 : spc1,spc2,spc1,spc2,spc4,spc1,spc2,spc5,spc3
+,spc1,spc1,spc2,spc2,spc3,spc1,spc2
GeneA,GeneB,GeneC,GeneD,GeneE,GeneF : spc4,spc5,spc1,spc2,spc1,spc2,sp
+c4,spc2,spc3,spc1
GeneX,GeneY,GeneP : spc6,spc8,spc6,spc7
GeneUnknown.,GeneUnknown. : spc1,spc2

Update: Added comment

[nerve]

Hi there,

Your code athough it has a bug or a error on my side providing incomplete details.

My sample input was
Gene1,Gene2,spc1,spc2
Gene3,Gene1,spc1,spc2,spc4
Gene4,Gene1,spc1,spc2,spc5,spc3,spc1
etc

And I got the correct results.

But the sample can contains entries like the below the number of "gene" is variable can be less or be more

GeneX,GeneY,GeneP,spc1,spc2
GeneY,spc3,spc4

The desired result would be
GeneX,GeneY,GeneP,spc1,spc2,spc3,spc4


But the results which the script gives is
GeneX,GeneY,spc3,GeneP,spc1,spc2,spc4

[Transient]

That's correct - my code assumes two genes per line in the first and second position. I had actually included a comment in my original attempt at solving the problem, but somehow left it out in my post =)

Update: Can it be assumed then, that a gene starts with "Gene" and the values start with "spc"?