Re^2: Clustering with Perl

The gene number can basically vary.
you can have <2 genes
Hi there,
Your code worked like a charm although 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 bellow

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

*************************************************************

Also how can i modify the cureent code to give me aoutput like this Sample input

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

Desired Result
GeneX,GeneY,GeneP,GeneZ,spc1=1,spc2=1,spc3=2,spc4=2

I want to count the number of \/ "spc" for a given "spc" /\ so that i can later confirm the output. because I have a 25 mb txt file to process which will probably take hour or more.

Comment on Re^2: Clustering with Perl

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Re^3: Clustering with Perl by dwm042 (Priest) on Jun 26, 2009 at 17:24 UTC
nerve, Looking at the things you want done, I don't see how code can tell that `GeneX,GeneY,GeneP,spc1,spc2 GeneY,spc3,spc4 GeneZ,spc3,spc4` [download] Should lead to: `Desired Result GeneX,GeneY,GeneP,GeneZ,spc1=1,spc2=1,spc3=2,spc4=2` [download] What in the data set "says" that GeneZ is to be clustered with X, Y, and P? Nothing that I can determine. The counts (e.g. spc1=1, etc) would be easy to do and the code I presented creates a stack of spc results. Just pop results off the stack, and count instances. David.	[reply] [d/l] [select]
Re^3: Clustering with Perl by dwm042 (Priest) on Jun 26, 2009 at 18:21 UTC
This is as close as I can come, given that the description of how to process data is inconsistent. The trick here is to partition the split data set into an array of genes and an array of spcs and work with that. I'm sure others here can make this prettier code than I. If you want it spaced nicely, please run a copy of perltidy on this code. #!/usr/bin/perl use warnings; use strict; # # %adjacent - is a hash of arrays. # each key contains a cluster identified by the key (root +). # %sequences - is a hash of hashes. # The first key is identical to a key (root) in %adjacent +. # The second key ids each "spcs" in the cluster. # The value is the count of "spc". # my %adjacent; my %sequences; while (<DATA>) { chomp; next unless $_ =~ /\w+/; my @component = split /\,/, $_; my @genes; my @spcs; for my $element (@component) { $element =~ s/\s+$//; if ( $element =~ /^Gene/i ) { push @genes, $element; } else { push @spcs, $element; } } if ( my $parent = rooted( \@genes ) ) { for my $gene (@genes) { push @{$adjacent{$parent}}, $gene unless ( has_root($gene)); } for my $species (@spcs) { $sequences{$parent}{$species}++; } } else { my $root = shift @genes; @{$adjacent{$root}} = (); for my $gene ( @genes ) { push @{$adjacent{$root}}, $gene unless ( has_root($gene)); } for my $species (@spcs) { $sequences{$parent}{$species}++; } } } print "----------------------------------------------\n"; for my $inner ( sort keys %adjacent ) { print "$inner"; for my $outer ( sort @{$adjacent{$inner}} ) { print ",$outer"; } for (sort keys %{$sequences{$inner}}) { printf ",%s=%d", $_, $sequences{$inner}{$_}; } 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; } sub rooted { my $aref = shift; for (@$aref) { my $parent = has_root( $_ ); return $parent if $parent; } 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,GeneY,GeneP,spc1,spc2 GeneY,spc3,spc4 [download] With the results: `C:\Code>perl adjacent.pl ---------------------------------------------- Gene1,Gene2,Gene3,Gene4,spc1=5,spc2=5,spc3=2,spc4=1,spc5=1 GeneA,GeneB,GeneC,GeneD,GeneE,GeneF,spc1=3,spc2=3,spc3=1,spc4=1 GeneX,GeneP,GeneY,spc1=1,spc2=1,spc3=1,spc4=1` [download]	[reply] [d/l] [select]