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Webservice-InterMine-Bio-0.9900
River stage zero No dependents
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/ Webservice::InterMine::Bio::GFFQuery

NAME

Webservice::InterMine::Bio::GFFQuery - GFF3 specific query behaviour.

SYNOPSIS

This module provides access to GFF3 results services for standard InterMine queries.

    use Webservice::InterMine::Bio qw/GFF3/;
    use Webservice::InterMine 'flymine';

    my $query = Webservice::InterMine->new_query(with => GFF3);
    $query->add_sequence_features("Gene", "Gene.exons", "Gene.transcripts");
    $query->add_constraint("Gene", "IN", "my_gene_list");

    my $feature_store = $query->get_feature_store(); # Get a Bio::DB::SeqFeature::Store

    $query->print_gff3(to => "my_genes.gff3");       # Print the results as GFF3

DESCRIPTION

This module extends InterMine queries with GFF3 specific functionality.

METHODS

get_feature_store()

Return a Bio::DB::SeqFeature::Store object loaded with data from the query. This method will first check for the availability of BioPerl functionality, but may throw an exception if this is not available. See Bio::DB::SeqFeature::Store.

get_gff3_iterator()

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.

get_gff3()

Return the string representation of the results of this query in GFF3 format.

get_gff3_uri()

Return the uri for the webservice to access the results of this query as fasta.

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 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.