Does this look right? (You may need to sort or uniq the gene names). 

C:\test>774383.pl
Gene1:Gene2 tags::
Group both under new tag: A

Gene3:Gene1 tags::A
Group first with second under A

Gene4:Gene1 tags::A
Group first with second under A

Gene2:Gene3 tags:A:A
Both grouped; add spcs

Gene2:Gene4 tags:A:A
Both grouped; add spcs

Gene3:Gene4 tags:A:A
Both grouped; add spcs

GeneA:GeneB tags::
Group both under new tag: B

GeneB:GeneC tags:B:
Group second with first under B

GeneC:GeneD tags:B:
Group second with first under B

GeneD:GeneE tags:B:
Group second with first under B

GeneE:GeneF tags:B:
Group second with first under B

GeneX:GeneY tags::
Group both under new tag: C

GeneX:GeneP tags:C:
Group second with first under C

{
  A => {
         genes => ["Gene1", "Gene2", "Gene3", "Gene4"],
         spcs  => [ 
             "spc1", "spc2", "spc1", "spc2", "spc4", "spc1", "spc2", "
+spc5", 
             "spc3", "spc1", "spc1", "spc2", "spc2", "spc3", "spc1", "
+spc2", 
         ],
       },
  B => {
         genes => ["GeneA", "GeneB", "GeneC", "GeneD", "GeneE", "GeneF
+"],
         spcs  => [ 
             "spc4", "spc5", "spc1", "spc2", "spc1", 
             "spc2", "spc4", "spc2", "spc3", "spc1", 
         ],
       },
  C => {
         genes => ["GeneX", "GeneY", "GeneP"],
         spcs  => ["spc6", "spc8", "spc6", "spc7"],
       },
}

[download]

The code: 

#! perl -s
use 5.010;
use strict;
use Data::Dump qw[ pp ];

=comment
My desired Output is
Gene1,Gene2,Gene3,Gene4,spc1,spc2,spc1,spc2,spc4,spc1,spc2,spc5,spc1,s
+pc2,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
=cut

my( $nextTag, %gTags, %groups ) =  'A';

while( <DATA> ) {
    chomp;
    my( $g1, $g2, @spcs ) = split ',';

    say "$g1:$g2 tags:$gTags{ $g1 }:$gTags{$g2 }"; <>;
    if( exists $gTags{ $g1 } and exists $gTags{ $g2 } ){
        if( $gTags{ $g1 } eq $gTags{ $g2 } ) {
            say "Both grouped; add spcs";
            ## Just add new spcs to existing
            push @{ $groups{ $gTags{ $g1 } }{ spcs } }, @spcs;
        }
        else { ## merge groups
            say "merge $gTags{ $g1 }:$gTags{$g2 }";
            ## Add the current info to the first gene group.
            push @{ $groups{ $gTags{ $g1 } }{ spcs  } }, @spcs;
            push @{ $groups{ $gTags{ $g1 } }{ genes } }, $g2;

            ## Move the info from the seconds gene group to the first
            push @{ $groups{ $gTags{ $g1 } }{ spcs  } }, 
                 @{ $groups{ $gTags{ $g2 } }{ spcs } };
            push @{ $groups{ $gTags{ $g1 } }{ genes } }, 
                 @{ $groups{ $gTags{ $g2 } }{ genes } };

            ## delete the second gene group
            $groups{ $gTags{ $g2 } } = undef;

            ## And re-tag it to be the first
            $gTags{ $g2 } = $gTags{ $g1 };
        }
    }
    elsif( exists $gTags{ $g1 } and not exists $gTags{ $g2 } ) {
        say "Group second with first under $gTags{ $g1 }";
        $gTags{ $g2 } = $gTags{ $g1 };
        push @{ $groups{ $gTags{ $g1 } }{ spcs } }, @spcs;
        push @{ $groups{ $gTags{ $g1 } }{ genes } }, $g2;
    }
    elsif( exists $gTags{ $g2 } and not exists $gTags{ $g1 } ) {
        say "Group first with second under $gTags{ $g2 }";
        $gTags{ $g1 } = $gTags{ $g2 };
        push @{ $groups{ $gTags{ $g2 } }{ spcs } }, @spcs;
        push @{ $groups{ $gTags{ $g2 } }{ genes } }, $g1;
    }
    else { ## neither yet exist so group them under a new tag
        my $tag = $nextTag++;
        say "Group both under new tag: $tag";
        $gTags{ $g1 } = $gTags{ $g2 } = $tag;
        push @{ $groups{ $tag }{ spcs  } }, @spcs;
        push @{ $groups{ $tag }{ genes } }, $g1, $g2;
    }
}

pp \%groups;


__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]
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
RIP PCW

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

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