now, here's a homework question!! :)
On Sat, Apr 23, 2011 at 10:27 AM, galeb abu-ali <abuali...@gmail.com> wrote:
> Hi,
>
> I'm trying to parse a table containing information about genes in a
> bacterial chromosome. Below is a sample for one gene, and there's about 4500
> such blocks in a file:
>
> gene_oid Locus Tag Source Cluster Information Gene
> Information E-value
> 642745051 SeSA_B0001 COG_category [T] Signal transduction
> mechanisms
> 642745051 SeSA_B0001 COG_category [K] Transcription
> 642745051 SeSA_B0001 COG1974 SOS-response transcriptional
> repressors (RecA-mediated autopeptidases) 2.0e-29
> 642745051 SeSA_B0001 pfam00717 Peptidase_S24 1.7e-13
> 642745051 SeSA_B0001 EC:3.4.21.- Hydrolases. Acting on peptide
> bonds (peptide hydrolases). Serine endopeptidases.
> 642745051 SeSA_B0001 KO:K03503 DNA polymerase V [EC:3.4.21.-]
> 0.0e+00
> 642745051 SeSA_B0001 ITERM:03797 SOS response UmuD protein. Serine
> peptidase. MEROPS family S24
> 642745051 SeSA_B0001 Locus_type CDS
> 642745051 SeSA_B0001 NCBI_accession YP_002112883
> 642745051 SeSA_B0001 Product_name protein SamA
> 642745051 SeSA_B0001 Scaffold NC_011092
> 642745051 SeSA_B0001 Coordinates 34..459(+)
> 642745051 SeSA_B0001 DNA_length 426bp
> 642745051 SeSA_B0001 Protein_length 141aa
> 642745051 SeSA_B0001 GC .52
>
>
>
>
> I want to parse information for Locus_Tag, Source, and Cluster Info for each
> gene so that the output table looks like this
>
>
> locus COG_category COG_category COGID Cluster_Information
>
> SeSA_B0001 [T] Signal transduction mechanisms [K] Transcription
> COG1974 SOS-response transcriptional repressors (RecA-mediated
> autopeptidases)
> SeSA_B0002 "\t" [L] Replication, recombination and repair COG0389
> Nucleotidyltransferase/DNA polymerase involved in DNA repair
>
>
> My problem is that some genes have 2 entries for COG_category, some only one
> and others none. I took a look at perldsc and tried to fit the table into
> one of the complex structures but didn't get far. Below is the code I came
> up with so far:
>
> #!/usr/bin/perl
> # parse_IMG_gene_info.pl
> use strict;
use warnings;
good, but no need to save space - you have a return key, put different
things on different lines unless you *really* fell it looks / reads
better to do otherwise.
>
>
> open( IN, "<", @ARGV ) or die "Failed to open: $!\n";
open( my $file, "<", $ARGV[ 0 ]) or die ".... $!\n";
>
> print "locus\tCOG_category\tCOG_category\tCOGID\tCluster_Information\n\n";
>
> my( %locus, @cogs, %cog_cat, %cog_id, $oid, $locus, $source, $cluster_info,
> $e );
>
> while( <IN> ) {
> if( $_=~ /COG_category/ ) {
> ( $oid, $locus, $source, $cluster_info ) = split "\t", $_;
> $cog_cat{ $locus } = $cluster_info;
> push( @cogs, { %cog_cat } );
> } elsif ( $_=~ /COG\d+/ ) {
> ( $oid, $locus, $source, $cluster_info ) = split "\t", $_;
> $cog_id{ $locus } = $cluster_info;
> }
> }
>
i don't really have the knowledge to help here, nor really want to
parse this. instead, i'll suggest using Text::CSV_XS, it's much easier
and will give you a good data structure, all you do to figure out a
column is there is 'if( $csv-[ $col ] ) { ..column has data.. }'
> close IN;
close $file;
or just let it go out of scope and close one its own.
>
> #print scalar @cogs, "\n";
>
> for my $test( sort keys %cog_cat ) {
> print "$test\t$cog_cat{ $test }\t$cog_id{ $test }\n";
> }
> print "\n";
can i suggest a database? it isn't that hard and will help tons in
future processing of the data and manipulation. also, a quick google
brought up some interesting results on your field:
http://oreilly.com/catalog/begperlbio/chapter/ch10.html
http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables/lib/Bio/ASN1/EntrezGene.pm
it might help to look at this (though, i think that Text::CSV will
suite your needs just fine):
http://oreilly.com/catalog/perlsysadm/chapter/ch09.html
--
To unsubscribe, e-mail: beginners-unsubscr...@perl.org
For additional commands, e-mail: beginners-h...@perl.org
http://learn.perl.org/
