NAME

Bio::Grep::Backend::Agrep - Agrep back-end

SYNOPSIS

  use Bio::Grep;
  
  my $sbe = Bio::Grep->new('Agrep');
  
  # generate a database. you have to do this only once. 
  $sbe->generate_database({ 
    file        => 'ATH1.cdna', 
    description => 'AGI Transcripts',
    datapath    => 'data',
  });
  
  # search for the reverse complement and allow 2 mismatches 
  # Don't calculate Alignments with EMBOSS
  $sbe->search({
    query   => 'GAGCCCTT',
    reverse_complement => 1, 
    mismatches         => 2,
    no_alignments      => 1,
    database           => 'ATH1.cdna',
  });
  
  my @internal_ids;
  
  # output the searchresults with nice alignments
  while ( my $res = $sbe->next_res) {
     print $res->sequence->id . "\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);

DESCRIPTION

Bio::Grep::Backend::Agrep searches for a query with agrep.

METHODS

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

CONSTRUCTOR

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

This method constructs an Agrep 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('Agrep');

PACKAGE METHODS

$sbe->available_sort_modes()

Returns all available sort modes as hash. keys are sort modes, values a short description.

Available sort modes in Agrep:

   currently none.
   

$sbe->is_tre_agrep()

Returns 1 if agrep binary is the one from the TRE library, 0 otherwise.

IMPORTANT NOTES

Database

Bio::Grep::Backend::RE databases are compatible with Bio::Grep::Backend::Agrep databases.

DIAGNOSTICS

See Bio::Grep::Backend::BackendI for other diagnostics.

Agrep call failed. Command was: ...

It was not possible to run agrep in function search(). Check the search settings. Agrep returns also exit(1) whenever no hit is found! 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.

Warning: Truncated record. Record is: ...

Can occur with long sequences and the WuManber or Glimpse Agrep implementation. The limit of record length can be changed by modifying the parameter Max_record in agrep.h.

SEE ALSO

Bio::Grep::Backend::BackendI Bio::Grep::SearchSettings Bio::SeqIO Bio::Index::Fasta

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENSE AND COPYRIGHT

Copyright (C) 2007-2009 by M. Riester.

Based on Weigel::Search v0.13, Copyright (C) 2005-2006 by Max Planck Institute for Developmental Biology, Tuebingen.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.