NAME
Bio::Grep::Backends::GUUGle - GUUGle back-end
SYNOPSIS
use Bio::Grep::Backends::GUUGle;
# construct the GUUGle back-end
my $sbe = Bio::Grep::Backends::GUUGle->new();
$sbe->settings->tmppath('tmp');
$sbe->settings->datapath('data');
# generate a GUUGle Bio::Grep database. you have to do this only once.
# GUUGle does not create a persistent index right now.
# This function generates an fast index for $sbe->get_sequences
# and files with a description and the alphabet (only DNA/RNA allowed)
$sbe->generate_database_out_of_fastafile('ATH1.cdna',
'AGI Transcripts (- introns, + UTRs)');
my %local_dbs_description = $sbe->get_databases();
my @local_dbs = sort keys %local_dbs_description;
# take first available database in our test
$sbe->settings->database($local_dbs[0]);
my $seq = 'UGAACAGAAAGCUCAUGAGCC';
# search for the reverse complement
$sbe->settings->query($seq);
$sbe->settings->reverse_complement(1);
# display 5 bases upstream and downstream of the match
$sbe->settings->upstream(5);
$sbe->settings->downstream(5);
$sbe->search();
# output all informations we have!
while ( my $res = $sbe->next_res ) {
print $res->sequence->id . "\n";
print $res->mark_subject_uppercase() . "\n";
print $res->alignment_string() . "\n\n";
}
DESCRIPTION
Bio::Grep::Backends::GUUGle searches for a query in a GUUGle suffix array.
NOTE 1: GUUGle always searches for the reverse complement. If you specify a query file, Bio::Grep throws an exception if reverse_complement is not set.
NOTE 2: GUUGle only allows search for exact matches. It counts GU as no mismatch.
METHODS
See Bio::Grep::Backends::BackendI for other methods.
- Bio::Grep::Backends::GUUGle->new()
-
This function constructs a GUUGle back-end object my $sbe = Bio::Grep::Backends::GUUGle->new(); $sbe->available_sort_modes()-
Returns all available sort modes as hash. keys are sort modes, values a short description.
$sbe->sort('ga');Available sortmodes in GUUGle:
ga : 'ascending order of dG' gd : 'descending order of dG'Note that 'ga' and 'gd' require that search results have dG set. Bio::Grep::RNA ships with filters for free energy calculation. Also note that these two sort options require that we load all results in memory.
DIAGNOSTICS
See Bio::Grep::Backends::BackendI for other diagnostics.
Bio::Root::SystemException-
It was not possible to run GUUGle in function
search.
Bio::Root::BadParameter
SEE ALSO
Bio::Grep::Backends::BackendI Bio::Grep::Container::SearchSettings Bio::Seq
AUTHOR
Markus Riester, <mriester@gmx.de>
LICENCE AND COPYRIGHT
Copyright (C) 2007 by M. Riester. All rights reserved.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
DISCLAIMER OF WARRANTY
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