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({ 
   file        => 'ATH1.cdna', 
   description => 'AGI Transcripts',
   datapath    => 'data',
 });
 
 # 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.

While doing a reverse-complement the query does not look like a...

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

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