NAME

Bio::Grep::Backend::RE - Perl Regular Expression back-end

SYNOPSIS

  use Bio::Grep;
  
  my $sbe = Bio::Grep->new('RE');
  
  $sbe->settings->datapath('data');
  
  # generate a database. you have to do this only once. 
  $sbe->generate_database('ATH1.cdna', 'AGI Transcripts (- introns, + UTRs)');
  
  # search on both strands  
  # retrieve up- and downstream regions of size 30
  
  $sbe->search({
    query   => 'GAGCCCTT',
    direct_and_rev_com => 1, 
    upstream           => 30,
    downstream         => 30,
    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->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);

  # sequences with at least 10 As
  $sbe->search({ query => '[A]{10,}' });
 
  # some SNPs
  $sbe->search({query => '[CG]TGC[AT]CTCTTCT[CG]TCA'});

DESCRIPTION

Bio::Grep::Backend::RE searches for a query with a Perl Regular Expression.

Note 1: BETA RELEASE!

Note 2: reverse_complement (and direct_and_rev_com ) are supported, but are only available for DNA/RNA queries, not for regular expressions.

Note 3: The i modifier is added to the regex. This means that the search is case insensitive.

Note 4: Be careful with RNA sequences: U is not the same as T in this back-end!

Note 5: Bio::Grep::Backend::RE databases are compatible with Bio::Grep::Backend::Agrep databases.

METHODS

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

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

This method constructs a RE 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('RE');
$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 RE:

                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.

Query does not look like a DNA/RNA sequence.

Either reverse_complement or direct_and_rev_com is set and the query does not match the regular expression m{\A [gactu]+ \z}xmsi. Bio::Root::BadParameter.

Query not defined.

You forgot to define $sbe->settings->query. Bio::Root::BadParameter.

SEE ALSO

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

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

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 LICENCE, 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.