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

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.

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:

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.