NAME

MS::DB::Search::Source::uniprot - interface for Uniprot downloads

SYNOPSIS

    use MS::DB::Search;

    my $db = MS::DB::Search->new();

    $db->add_from_source(
        source           => 'uniprot',
        taxid            => '12345',
        ref_only         => 1,
        reviewed_only    => 0,
        include_isoforms => 0,
    );

DESCRIPTION

MS::DB::Search::Source::uniprot provides an interface to the Uniprot database for fetching proteomes based on taxonomic ID. It is not intended to be called directly, but rather used via the 'source' argument to the MS::DB::Search add_from_source method.

ARGUMENTS

The following arguments should be provided to the MS::DB::Search add_from_source method call:

source <plugin>

Should be 'uniprot'

taxid <id>

A numeric NCBI taxonomic ID for the organim of interest (one of 'taxid' or 'proteome' is required)

proteome <id>

A Uniprot ID for the proteome of interest (one of 'taxid' or 'proteome' is required)

ref_only <bool>

Whether to only fetch reference proteomes (default: 0)

reviewed_only <bool>

Whether to only fetch reviewed protein sequences (default: 0)

include_isoforms <bool>

Whether to include protein isoform sequences in the dataset (default: 0)

CAVEATS AND BUGS

Please report bugs to the author.

AUTHOR

Jeremy Volkening <jdv@base2bio.com>

COPYRIGHT AND LICENSE

Copyright 2016 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.