Summary

G::Seq::Operon - Perl extension for blah blah blah

Package variables

Included modules

Inherit

Exporter

Synopsis

  use G::Seq::Operon;
  blah blah blah

Description

Stub documentation for G::Seq::Operon was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.
Blah blah blah.

Methods

Methods description

  Name: set_operon   -   set operon information from RegulonDB

  Description:
    This program retrieves the operon information from RegulonDB, and adds this
    to the given genome data. !!!This method currently only works for E.coli!!!

    Two attributes are added to each CDS hash.
        $genome->{$cds}->{operon}
    contains the name of the operon to which the gene belongs, and 
        $genome->{$cds}->{operonN}
    contains the rank order of the gene within the operon.

  Usage:
    set_operon($gb);

 Options:
   None.

  References:
   1. Salgado H et al. (2006) "RegulonDB (version 5.0): Escherichia coli K-12 transcriptional
      regulatory network, operon organization, and growth conditions", Nucleic Acids Res. 
      1;34(Database issue):D394-7

  Author: 
    Kazuharu Arakawa (gaou@sfc.keio.ac.jp)

  History:
   20070829-01 patched to match latest version of RegulonDB formamt
               (patch by Hiroyuki Nakamura <t04632hn@sfc.keio.ac.jp>
   20061003-01 updated to use data from RegulonDB
   20020207-01 initial posting

Methods code

sub set_operon {

    my @args = opt_get(@_);
    my $gb = shift @args;

    if ($gb->{LOCUS}->{id} eq 'U00096' || $gb->{LOCUS}->{id} eq 'NC_000913'){

	my $url = "http://regulondb.ccg.unam.mx:80/data/OperonSet.txt";
	my $dir = $ENV{HOME} . '/.glang/data/OperonSet.txt';
	mirror($url, $dir);
	die("setOperon: cannot retrieve data from RegulonDB.") unless(-e $dir);

	my $flag = 0;
	open(FILE, $dir) || die($!);
	while (<FILE>) {
	    chomp;

	    if (/^Columns\:/) {
	      $flag++;
	      next;
	    }
	    elsif(/^\t\(\d\)\s/) {
	      $flag++;
	      next;
	    }

	    if($flag == 5){

		my %geneOrder;

		my ($operon, $num, $direction, $genes) = split(/\t/, $_, 4);
		next unless($num >= 2);

		foreach my $genepair (split(/,/, $genes)){
		    my ($gene, $locustag) = split(/\|/, $genepair, 2);
		    my $cds = $gb->gene2id($locustag);

		    $cds = $gb->gene2id($gene) unless(length $cds);

		    if($cds){
			$gb->{$cds}->{operon} = $operon;
			$geneOrder{$cds} = $gb->{$cds}->{start};
		    }
		}

		my $i = 1;
		if($direction eq 'forward'){
		    foreach my $cds (sort {$geneOrder{$a} <=> $geneOrder{$b}} keys %geneOrder){
			$gb->{$cds}->{operonN} = $i;
			$i ++;
		    }
		}else{
		    foreach my $cds (sort {$geneOrder{$b} <=> $geneOrder{$a}} keys %geneOrder){
			$gb->{$cds}->{operonN} = $i;
			$i ++;
		    }
		}

	    }else{
		msg_error($_, "\n");
	    }
	}
	close(FILE);

	foreach my $cds ($gb->cds()){
	    $gb->{$cds}->{operonN} = 0 unless(length $gb->{$cds}->{operon});
	}

   }else{
       msg_error("No Operon data for this species.\n\n");
   }

    return 1;

}

General documentation

A. U. Thor, a.u.thor@a.galaxy.far.far.away

perl(1).