NAME

Bio::Grep::Backend::GUUGle - GUUGle back-end

SYNOPSIS

  use Bio::Grep;
  
  my $sbe = Bio::Grep->new('GUUGle');
  
  $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('ATH1.cdna', 
     'AGI Transcripts (- introns, + UTRs)');
 
  # search on both strands (GU allowed) 
  # retrieve up- and downstream regions of size 30
  $sbe->search({
    query   => 'GAGCCCTTGGGGGGG',
    direct_and_rev_com => 1, 
    upstream           => 30,
    downstream         => 30,
    gumismatches       => 0,
    database           => 'ATH1.cdna',
  });

  my @internal_ids;

  # 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";
     push @internal_ids, $res->sequence_id;
  }
  
  # get the complete sequences as Bio::SeqIO object
  my $seq_io = $sbe->get_sequences(\@internal_ids);
  
  # search for targets (GU allowed)
  $sbe->search({
    query   => 'GAGCCCTTGGGGGGG',
    reverse_complement => 1, 
    gumismatches       => 0,
  });

DESCRIPTION

Bio::Grep::Backend::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::Backend::BackendI for inherited methods.

Bio::Grep::Backend::GUUGle->new()

This method constructs a GUUGle back-end object and should not used directly. Rather, a back-end should be constructed by the main class Bio::Grep:

  my $sbe = Bio::Grep->new('GUUGle');
$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::Backend::BackendI for other diagnostics.

GUUGle call failed. Command was: ...

It was not possible to run GUUGle in function search(). Check the search settings. If you want to reproduce the system() call, you can set the environment variable BIOGREPDEBUG. If this variable is set, then the temporary files won't get deleted. Bio::Root::SystemException.

GUUGle searches only for the reverse complement.

You have specified a query file and reverse_complement is not set. Bio::Root::BadParameter.

query_length not set. See -d flag in the...

You have specified a query file and forgot to set query_length. Bio::Root::BadParameter.

SEE ALSO

Bio::Grep::Backend::BackendI Bio::Grep::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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