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.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

cpanm NCBIx::Geo

perl -MCPAN -e shell
install NCBIx::Geo