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Re: Clustering with Perl

by Transient (Hermit)
on Jun 24, 2009 at 15:38 UTC ( #774432=note: print w/replies, xml ) Need Help??


in reply to Clustering with Perl

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

Replies are listed 'Best First'.
Re^2: Clustering with Perl
by nerve (Initiate) on Jun 25, 2009 at 01:22 UTC
    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
      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"?

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