NAME

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

SYNOPSIS

  use Bio::Grep::Backend::Agrep;
  
  # configure our search back-end, in this case Agrep
  my $sbe = Bio::Grep::Backend::Agrep->new();
  
  $sbe->settings->execpath('/usr/bin');
  $sbe->settings->tmppath('tmp');
  $sbe->settings->datapath('data_agrep');
  
  # generate a database. you have to do this only once. 
  $sbe->generate_database('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 and allow 4 mismatches
  $sbe->settings->query($seq);
  $sbe->settings->reverse_complement(1);
  $sbe->settings->mismatches(4);
  
  # things should be fast? then turn alignment calculation off
  $sbe->settings->no_alignments(1);
  
  # now try to search, agrep back-end will also throw an exception if no hit
  # was found
  $sbe->search();
  
  # output the searchresults with nice alignments
  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::Backend::Agrep searches for a query with agrep.

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

METHODS

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

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

This function constructs an agrep back-end object

   my $sbe = Bio::Grep::Backend::Agrep->new();

$sbe->available_sort_modes()

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

Available sortmodes in Agrep:

   currently none.
   

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.

SEE ALSO

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

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENCE AND COPYRIGHT

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

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