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Webservice-InterMine-Bio-0.9800
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/ Webservice::InterMine::Bio

NAME

Webservice::InterMine::Bio - Access data from InterMine queries in biological formats.

VERSION

Version 0.98

SYNOPSIS

This module provides roles that can be used to access data in standard biological formats, and even interface directly with BioPerl classes.

use Webservice::InterMine::Bio qw/BIO_PERL/;
use Webservice::InterMine 'flymine';

my $query = Webservice::InterMine->new_query(with => BIO_PERL);
$query->add_sequence_features("Gene", "Gene.exons", "Gene.transcripts");
my $feature_store = $query->get_feature_store(); # Get a Bio::DB::SeqFeature::Store
...

EXPORT

This module exports (optionally) constants that simplify references to the roles in this package, by providing means to name these roles in the manner expected by new_query. So:

  • GFF3 => ['Webservice::InterMine::Bio::GFFQuery']

  • FASTA => ['Webservice::InterMine::Bio::FastaQuery']

  • BED => ['Webservice::InterMine::Bio::BEDQuery']

  • BIO_PERL => [ all... ]

AUTHOR

Alex Kalderimis, <dev at intermine.org>

BUGS

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.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc Webservice::InterMine::Bio

You can also look for information at:

ACKNOWLEDGEMENTS

The funding bodies that support InterMine:

LICENSE AND COPYRIGHT

Copyright 2011 Alex Kalderimis.

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.