This code will cluster your "genes".. I do not know how far it goes to allow you to solve the second part of your problem.

#!/usr/bin/perl

use warnings;
use strict;
my %adjacent;
while (<DATA>) {
    my @component = split /\,/, $_, 3;
    my $parent;
    if ( defined($adjacent{$component[0]})) {
        $adjacent{$component[0]}{$component[1]} = $component[2];
    }
    elsif ( defined($adjacent{$component[1]})) {
        $adjacent{$component[1]}{$component[0]} = $component[2];
    }
    elsif ( $parent = has_parent($component[0]) ) {
    $adjacent{$parent}{$component[1]} = $component[2];
    }
    elsif ( $parent = has_parent($component[1]) ) {
    $adjacent{$parent}{$component[0]} = $component[2];
    }
    else {
        $adjacent{$component[0]}{$component[1]} = $component[2];
    }
}
print "\n\n*----------------------------------------------*\n";
for my $inner ( sort keys %adjacent ) {
    print "$inner ";
    for my $outer ( sort keys %{$adjacent{$inner}} ) {
        print ", $outer";
    }
    print "\n";
}

sub has_parent {
    my $candidate = shift;
    for my $inner ( sort keys %adjacent ) {
    for my $outer ( sort keys %{$adjacent{$inner}} ) {
        if ( $candidate eq $outer ) {
        return $inner;
        }
    }
    }
    return 0;    
}


__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

[download]
And the results are:

C:\Code>perl adjacent.pl

*----------------------------------------------*
Gene1 , Gene2, Gene3, Gene4
GeneA , GeneB, GeneC, GeneD, GeneE, GeneF
GeneX , GeneP, GeneY

[download]
Update: newer code solves it completely.

#!/usr/bin/perl

use warnings;
use strict;
#
# %adjacent  - each key contains a cluster identified by the key (root
+).
# %sequences - contains sequences of "spcs" for each cluster.
#
my %adjacent;
my %sequences;
while (<DATA>) {
    chomp;
    my @component = split /\,/, $_, 3;
    my $parent;
    $component[2] =~ s/\s+$//;
    if ( $parent = has_root($component[0]) ) {
    push @{$adjacent{$parent}}, $component[1] 
        unless ( has_root($component[1]));
    push @{$sequences{$parent}}, $component[2];
    }
    elsif ( $parent = has_root($component[1]) ) {
    push @{$adjacent{$parent}}, $component[0]
        unless ( has_root($component[0]));
    push @{$sequences{$parent}}, $component[2];
    }
    else {
        push @{$adjacent{$component[0]}}, $component[1];
    push @{$sequences{$component[0]}}, $component[2];
    }
}
print "*----------------------------------------------*\n";
for my $inner ( sort keys %adjacent ) {
    print "$inner";
    for my $outer ( sort @{$adjacent{$inner}} ) {
        print ",$outer";
    }
    for (@{$sequences{$inner}}) {
        print ",$_";
    }        
    print "\n";
}
sub has_root {
    my $candidate = shift;
    return 0 if ( keys %adjacent < 1);
    for my $inner ( sort keys %adjacent ) {
    if ( $candidate eq $inner ) {
        return $inner;
    }
    for my $outer ( sort @{$adjacent{$inner}} ) {
        if ( $candidate eq $outer ) {
        return $inner;
        }
    }
    }
    return 0;    
}


__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

[download]

In reply to Re: Clustering with Perl by dwm042
in thread Clustering with Perl by nerve

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