NAME
NCBIx::Geo - Download and Compare Transcripts through NCBI GEO
VERSION
This document describes NCBIx::Geo version 1.0.0
SYNOPSIS
To use the script, first install it as described in README. Then check usage:
geo -h
To get sample data related to a GDS, GSE, or GSM:
geo -v -a <accn> -d <data_dir>
To compare transcripts:
geo -v -a <accn> -c <accn> -d <data_dir>
If you use NCBIx::Geo in a custom perl script, you can access the individual values of each transcript. To use NCBIx::Geo in a custom perl script:
use NCBIx::Geo;
# Load meta-data and ensure that all sample data is downloaded
my $geo = NCBIx::Geo->new({ accn => 'GDS1096', data_dir => '/home/roger/geo/data/', data => 1, debug => 1 });
# Print the transcript_id diff between two or more samples
print $geo->diff({ list => ['GSM44705', 'GSM44704'] });
# Load meta-data first
my $geo = NCBIx::Geo->new({ accn => 'GDS1096', data_dir => '/home/roger/geo/data/' });
# Print a description and summary of the accession
print $geo->desc();
# Get all related sample data for accn if you haven't already
$geo->data();
# Long way around but flexible
my $geo = NCBIx::Geo->new();
$geo->meta({ accn => 'GDS1096' });
$geo->data();
# Get transcript values
my $sample = $geo->sample({ accn => 'GSM44705' });
my @transcripts = @{ $sample->transcript_ids() };
foreach my $transcript_id ( @transcripts ) {
print "\n$transcript_id =>\n";
print $sample->value({ transcript_id => $transcript_id }) . "\n";
print $sample->call({ transcript_id => $transcript_id }) . "\n";
print $sample->p_value({ transcript_id => $transcript_id }) . "\n";
}
DESCRIPTION
NCBIx::Geo uses eUtils, the GEO acc.cgi script, and supplementary data via ftp to download, describe, and compare transcripts of gene abundance measurement.
CONFIGURATION AND ENVIRONMENT
The geo.pp script should be copied to an executable directory in your PATH environment variable. It should be renamed geo.
DEPENDENCIES
Class::Std
Class::Std::Utils
LWP::Simple
XML::Simple
Data::Dumper
Getopt::Long
INCOMPATIBILITIES
None reported.
BUGS AND LIMITATIONS
No bugs have been reported.
Please report any bugs or feature requests to bug-ncbix-geo@rt.cpan.org
, or through the web interface at http://rt.cpan.org.
AUTHOR
Roger A Hall <rogerhall@cpan.org>
LICENSE AND COPYRIGHT
Copyleft (c) 2010, Roger A Hall <rogerhall@cpan.org>
. All rights reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See perlartistic.
DISCLAIMER OF WARRANTY
BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.
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