NAME

Webservice::InterMine::Bio::FastaQuery - FASTA specific query behaviour.

SYNOPSIS

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

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

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

    my $feature_store = $query->get_seq_io(); # Get a Bio::SeqIO object representing the sequence

    $query->print_fasta(to => "my_genes.fa"); # Print the results as FASTA

DESCRIPTION

This module extends InterMine queries with GFF3 specific functionality.

METHODS

get_seq_io()

Return a Bio::SeqIO 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::SeqIO.

get_fasta_iterator()

Return a results iterator for this query in FASTA format.

get_fasta()

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

print_fasta(to => $file)

Print the results of this query in FASTA format to the file requested.

get_fasta_uri()

Get the uri of the webservice that provides results in FASTA format.

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