Webservice::InterMine::Bio::BEDQuery - BED specific query behaviour.
This module provides access to BED results services for standard InterMine queries.
use Webservice::InterMine::Bio qw/BED/; use Webservice::InterMine 'flymine'; my $query = Webservice::InterMine->new_query(with => BED); $query->add_sequence_features("Gene", "Gene.exons", "Gene.transcripts"); $query->add_constraint("Gene", "IN", "my_gene_list"); $query->print_bed(to => "my_genes.bed"); # Print the results as BED
This module extends InterMine queries with BED specific functionality.
Whether or not to prefix "chr" to each chromosome. Defaults to true.
A description of the track. If none is provided the webservice will generate one.
Return a results iterator for this query in GFF3 format.
Print the results of this query as GFF3 to a file, or to the screen if no file is provided.
Return the string representation of the results of this query in GFF3 format.
Return the uri for the webservice to access the results of this query as fasta.
modified to add compatibility and track descriptions if required.
<dev at intermine.org>
Please report any bugs or feature requests to
bug-webservice-intermine-bio at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Webservice-InterMine-Bio. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
You can find documentation for this module with the perldoc command.
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The funding bodies that support InterMine:
Copyright 2011 InterMine
This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.
See http://dev.perl.org/licenses/ for more information.