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Revision 1.1 - (download) (as text) (annotate)
Mon Apr 4 20:55:07 2011 UTC (8 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_release_3_0_4, mgrast_dev_06072011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, rast_rel_2014_0729, mgrast_dev_05262011, mgrast_release_3_1_2, mgrast_release_3_1_1, rast_rel_2011_0928, mgrast_dev_04132011, mgrast_dev_04052011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_10262011, mgrast_dev_04082011, mgrast_release_3_1_0, mgrast_release_3_0_3, HEAD
Added to allow retrieval of pegs in atomic regulons.

#!/usr/bin/perl -w
use strict;

use Getopt::Long;
use SAPserver;
use ScriptThing;
use SeedEnv;

#	This is a SAS Component.

=head1 svr_atomic_regulons

    svr_atomic_regulons -g genome >experiments.tbl

List all the atomic regulons computed for a specified genome or for all genomes lists
in a file.

This script takes as input one or more genomes and for each genome lists all the
atomic regulons associated with it along with their component pegs. The input
should be a tab-delimited file with genome IDs in the last column. The output
file will have an two additional columns containing the atomic regulon ID and the
peg ID, respectively.

This is a pipe command. The input is from the standard input and the output is
to the standard output. The number of output lines will in general be far greater
than the number of input genomes.

=head2 Command-Line Options

=over 4

=item url

The URL for the Sapling server, if it is to be different from the default.

=item c

Index (1-based) of the input column containing the genome ID. If omitted, the
last column of the input will be used.

=item g

ID of a genome. If this option is specified, then the output file will contain
two columns, with the incoming genome ID in the first column of every line and
the second column containing the experiment IDs. The standard input will not
be read.



# Parse the command-line options.
my $url;
my $genomeID;
my $column;
my $inputFile = "-";
my $opted =  GetOptions('url=s' => \$url, "g=s" => \$genomeID, "c=i" => \$column,
                        "i=s" => \$inputFile);
# Check for errors.
if (! $opted) {
    print "usage: svr_atomic_regulons [--url=http://...] [-g genomeID] [-c col] <input >output\n";
} else {
    # Get the server object.
    my $sapObject = SAPserver->new(url => $url);
    # Get the input genomes. This will either be in the form of an open file
    # handle or a singleton list. The GetBatch method knows what to do in
    # either case.
    my $ih;
    if ($genomeID) {
        # We have a genome ID, so it's passed in as a list.
        $ih = [$genomeID];
    } else {
        # Here we have an input file.
        open($ih, "<$inputFile") || die "Cannot open genome file: $!";
    # The main loop processes chunks of input, 10 lines at a time.
    while (my @tuples = ScriptThing::GetBatch($ih, 10, $column)) {
        # Loop through the tuples, computing the results. The relevant server method
        # onlt accepts one genome at a time, which is quite different from the norm.
        for my $tuple (@tuples) {
            # Get the genome ID and the input line.
            my ($genome, $line) = @$tuple;
            # Get the hash of atomic regulons for this genome.
            my $regulonH = $sapObject->atomic_regulons(-id => $genome);
            # Loop through the regulons found.
            for my $regulon (sort keys %$regulonH) {
                my $pegs = $regulonH->{$regulon};
                # Loop through the pegs in this regulon, writing output lines.
                for my $peg (@$pegs) {
                    print "$line\t$regulon\t$peg\n";

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