NCBIx::Geo::Base - Download and Compare Transcripts through NCBI GEO
This document describes NCBIx::Geo::Base version 1.0.0
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"; }
Roger A Hall <rogerhall@cpan.org>
<rogerhall@cpan.org>
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.
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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To install NCBIx::Geo, copy and paste the appropriate command in to your terminal.
cpanm
cpanm NCBIx::Geo
CPAN shell
perl -MCPAN -e shell install NCBIx::Geo
For more information on module installation, please visit the detailed CPAN module installation guide.