NAME

Webservice::InterMine::Bio::SequenceFeatureQuery - Common behaviour for queries on sequence features.

SYNOPSIS

This module provides Sequence Feature specific behaviour for InterMine queries.

    use Webservice::InterMine 'flymine';

    my $query = Webservice::InterMine->new_query(
        with => 'Webservice::InterMine::Bio::SequenceFeatureQuery'
    );

    $query->add_sequence_features("Gene", "Gene.exons", "Gene.transcripts");
    ...

DESCRIPTION

This module is used by GFF3 and Fasta queries to provide common sequence feature specific functionality. It is not really useful on its own.

METHODS

add_sequence_features(Path...)

Add sequence features to the output of the current query. All paths provided must be valid view paths, and evaluate to represent a SequenceFeature or a class that inherits from SequenceFeature.

  $query->add_sequence_features("Gene", "Gene.exon");

get_seq_iterator($format)

Return a result iterator for a sequence feature query.

get_sequence_uri($format)

Return the resource uri for a particular kind of sequence feature query.

get_sequence($format)

Get a string representing the sequence in the format requested.

print_seq(format => $format, to => $fh, compress => $compress)

Prints the requested sequence query in the requested format to the requested location, or STDOUT if none is provided. If the location is a filename, and it ends in 'gz', then compression will be requested, whether or not the parameter was present.

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