NAME

Webservice::InterMine::Bio::BEDQuery - BED specific query behaviour.

SYNOPSIS

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

DESCRIPTION

This module extends InterMine queries with BED specific functionality.

ucsc_compatible

Whether or not to prefix "chr" to each chromosome. Defaults to true.

track_description

A description of the track. If none is provided the webservice will generate one.

get_bed_iterator()

Return a results iterator for this query in GFF3 format.

print_bed(to => $file)

Print the results of this query as GFF3 to a file, or to the screen if no file is provided.

get_bed()

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

get_bed_uri()

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

get_request_parameters

modified to add compatibility and track descriptions if required.

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:

• RT: CPAN's request tracker

  http://rt.cpan.org/NoAuth/Bugs.html?Dist=Webservice-InterMine-Bio

• AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/Webservice-InterMine-Bio

• CPAN Ratings

  http://cpanratings.perl.org/d/Webservice-InterMine-Bio

• Search CPAN

  http://search.cpan.org/dist/Webservice-InterMine-Bio/

ACKNOWLEDGEMENTS

The funding bodies that support InterMine:

• The Wellcome Trust http://www.wellcome.ac.uk/

• The NIH/NHGRI http://www.nih.gov/

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.

cpanm Webservice::InterMine::Bio

perl -MCPAN -e shell
install Webservice::InterMine::Bio