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Bio-Grep-v0.10.6
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/ Bio::Grep

NAME

Bio::Grep - Perl extension for searching in DNA and Protein sequences

VERSION

This document describes Bio::Grep version 0.10.6

SYNOPSIS

  use Bio::Grep;
  
  my $sbe = Bio::Grep->new('Vmatch');   
  
  # define the location of the suffix arrays
  $sbe->settings->datapath('data');
  
  mkdir($sbe->settings->datapath);      
  
  # now generate a suffix array. you have to do this only once.
  $sbe->generate_database({
     file => 'ATH1.cdna',
     description => 'AGI Transcripts',
  });
  
  # search in this suffix array
  $sbe->settings->database('ATH1.cdna');
  
  # search for the reverse complement and allow 2 mismatches
  $sbe->settings->query('UGAACAGAAAG');
  $sbe->settings->reverse_complement(1);
  $sbe->settings->mismatches(2);

  # or you can use Fasta file with queries
  # $sbe->settings->query_file('Oligos.fasta');

  # $sbe->search();

  # Alternatively, you can specify the settings in the search call.
  # This also resets everything except the paths and the database
  # (because it is likely that they don't change when search is called
  # multiple times)

  $sbe->search( { query  =>  'AGAGCCCT',
                  reverse_complement => 1,
                  mismatches         => 1,
                 });  
  
  my @ids;

  while ( my $res = $sbe->next_res ) {
     print $res->sequence->id . "\n";
     print $res->alignment_string() . "\n\n";
     push @ids, $res->sequence_id;
  }
  
  # get the gene sequences of all matches as Bio::SeqIO object.
  # (to generate a Fasta file for example)
  my $seqio = $sbe->get_sequences(\@ids);

DESCRIPTION

Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios (for example whole genome, protein and RNA data). Bio::Grep provides a common API to the most popular tools. This way, you can easily switch or combine tools.

METHODS

CONSTRUCTOR

new($backend)

This method constructs a Bio::Grep back-end object. Available external back-ends are Vmatch, Agrep, and GUUGle. Perl regular expressions are available in the RE back-end. Vmatch is default.

Sets temporary path to File::Spec->tmpdir();

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

Returns an object that uses Bio::Grep::Backend::BackendI as base class. See Bio::Grep::Backend::BackendI, Bio::Grep::Backend::Vmatch, Bio::Grep::Backend::Agrep, Bio::Grep::Backend::GUUGle and Bio::Grep::Backend::RE.

FEATURES

  • Bio::Grep supports most of the features of the back-ends. If you need a particular feature that is not supported, write a feature request. In general it should be easy to integrate. For a complete list of supported features, see Bio::Grep::SearchSettings, for an overview see "FEATURE COMPARISON".

  • This module should be suitable for large data sets. The back-end output is piped to a temporary file and the parser only stores the current hit in memory.

  • Bio::Grep includes an interface for search result filters. See "FILTERS". This module also allows you to retrieve up- and downstream regions. Together with filters, this makes Bio::Grep an ideal framework for seed and extend algorithms.

  • Bio::Grep was in particular designed for web services and therefore checks the settings carefully before calling back-ends. See "SECURITY".

QUICK START

This is only a short overview of the functionality of this module. You should also read Bio::Grep::Backend::BackendI and the documentation of the back-end you want to use (e.g. Bio::Grep::Backend::Vmatch).

Bio::Grep::Cookbook is a (not yet comprehensive) collection of recipes for common problems.

GENERATE DATABASES

As a first step, you have to generate a Bio::Grep database out of your Fasta file in which you want to search. A Bio::Grep database consists of a couple of files and allows you to retrieve information about the database as well as to perform queries as fast and memory efficient as possible. You have to do this only once for every file.

For example:

  my $sbe = Bio::Grep->new('Vmatch');   

  $sbe->generate_database({
     file => 'ATH1.cdna',
     datapath    => 'data', 
     description => 'AGI Transcripts',
  });

Now, in a second script:

  my $sbe = Bio::Grep->new('Vmatch');   
  $sbe->settings->datapath('data');

  my %local_dbs_description = $sbe->get_databases();
  my @local_dbs = sort keys %local_dbs_description;

Alternatively, you can use bgrep which is part of this distribution:

  bgrep --backend Vmatch --database TAIR6_cdna_20060907 --datapath data --createdb

SEARCH SETTINGS

All search settings are stored in the Bio::Grep::SearchSettings object of the back-end:

  $sbe->settings

To set an option, call

  $sbe->settings->optionname(value)

For example

  $sbe->settings->datapath('data');
  # take first available database 
  $sbe->settings->database($local_dbs[0]);
  $sbe->settings->query('AGAGCCCT');

See the documentation of your back-end for available options.

SEARCH

To start the back-end with the specified settings, simply call

  $sbe->search();

This method also accepts an hash reference with settings. In this case, all previous defined options except all paths and the database are set to their default values.

  $sbe->search({ mismatches => 2, 
                 reverse_complement => 0, 
                 query => 'AGAGCCCT' });

ANALYZE SEARCH RESULTS

Use such a Bio::Perl like while loop to analyze the search results.

  while ( my $res = $sbe->next_res ) {
     print $res->sequence->id . "\n";
     print $res->alignment_string() . "\n\n";
  }

See Bio::Grep::SearchResult for all available information.

BGREP

This distribution comes with a sample script called bgrep.

WHICH BACK-END?

We support these external back-ends:

Vmatch

http://vmatch.de/

Agrep

ftp://ftp.cs.arizona.edu/agrep/ (original Wu-Manber 1992 implementation for UNIX), http://www.tgries.de/agrep/ (DOS, Windows, OS/2), http://webglimpse.net/download.php (Agrep binary of Glimpse) and http://laurikari.net/tre/download.html (TRE implementation).

GUUGle

http://bibiserv.techfak.uni-bielefeld.de/guugle/

FEATURE COMPARISON

FeatureAgrepGUUGleREVmatch
Suffix Arrays/Trees no yes no yes
Sliding Window yes no yes no
Persistent Index1 no no no yes
Mismatches yes no no yes
Edit Distance yes no no yes
Insertions no no no no
Deletions no no no no
Multiple Queries2 no yes no yes
GU no yes no no
DNA/RNA yes yes yes yes
Protein yes no yes yes
Direct and Revcom no yes yes yes
Reverse Complement yes yes yes yes
Upstream/Downstream no yes yes yes
Filters no yes yes yes
Query Length3 no yes no yes
Regular Expressions4 no no yes no

1Needs pre-calculation and (much) more memory but queries are in general faster
2With query_file
3Matches if a substring of the query of size n or larger matches
4Agrep soon

Vmatch is fast but needs a lot of memory. Agrep is the best choice if you allow many mismatches in short sequences, if you want to search in Fasta files with relatively short sequences (e.g CDNA or Protein databases) and if you are only interested in which sequences the approximate match was found. Its performance is in this case amazing. If you want the exact positions of a match in the sequence, choose Vmatch. If you want nice alignments, choose Vmatch too (EMBOSS can automatically align the sequence and the query in the Agrep back-end, but then Vmatch is faster). Filters require exact positions, so you can't use them with Agrep. This may change in future version or not. The Agrep implementation of the TRE library (http://laurikari.net/tre/) is also supported. This implementation has less limitations and more features (e.g. you get the exact hit positions) but is much slower. See Bio::Grep::Benchmarks.

GUUGle may be the best choice if you have RNA queries (counts GU as no mismatch) and if you are interested in only exact matches. Another solution here would be to use Vmatch and write a filter (see next section) that only allows GU mismatches. Of course, this is only an alternative if you can limit ($sbe->settings->mismatches()) the maximal number of GU mismatches. Vmatch with its pre-calculated suffix arrays is really fast, so you should consider this option.

Perl regular expressions are available in the RE back-end. It is a very simple back-end which is written in pure Perl and which does not require any additional software.

FILTERS

Filtering search results is a common task. For that, Bio::Grep provides an filter interface, Bio::Grep::Filter::FilterI. Writing filters is straightforward:

   package MyFilter;
   
   use strict;
   use warnings;
   
   use Bio::Grep::Filter::FilterI;
   
   use base 'Bio::Grep::Filter::FilterI';
   
   use Class::MethodMaker
    [ new => [ qw / new2 / ],
      ... # here some local variables, see perldoc Class::MethodMaker
    ];
   
   sub new {
      my $self = shift->new2;
      $self->delete(1); # a filter that actually filters, not only adds
                        # remarks to $self->search_result->remark

      $self->supports_alphabet( dna => 1, protein => 1);
      $self;
   }
   
   sub filter {
      my $self = shift;
      # code that examines $self->search_result
      # and returns 0 (not passed) or 1 (passed)
      ...
      $self->message('passed');
      return 1;
   }   
   
   sub reset_filter {
      my $self = shift;
      # if you need local variables, you can clean up here
   }

   1;# Magic true value required at end of module

To apply your filter:

   ...

   my $filter = MyFilter->new();

   $sbe->settings->filters( ( $filter ) );
   $sbe->search();

See Bio::Grep::Filter::FilterI.

ERROR HANDLING

Bio::Grep throws Bio::Perl exceptions when errors occur. You can use the module Error to catch these exceptions:

   use Error qw(:try);
  
   ...
  
   try {
       $sbe->search();
   } catch Bio::Root::SystemException with {
       my $E = shift;
       print STDERR 'Back-end call failed: ' .     
       $E->{'-text'} . ' (' .  $E->{'-line'} . ")\n";
       exit(1);    
   } catch Bio::Root::BadParameter with {
       my $E = shift;
       print STDERR 'Wrong Settings: ' .     
       $E->{'-text'} . ' (' .  $E->{'-line'} . ")\n";
       exit(1);    
   } otherwise {        
       my $E = shift;
       print STDERR "An unexpected exception occurred: \n$E";
       exit(1);  
   };

Bio::Grep throws a SystemException when a system() call failed, BadParameter whenever Bio::Grep recognizes some problems in the settings. Be aware that Bio::Grep does not find all of these problems. In such a case, the back-end call will fail and this module will throw a SystemException.

Whenever it is not possible to open, copy, close, delete or write a file, croak() (Carp) is called.

See Bio::Root::Exception, Carp.

SECURITY

The use of this module (in Web Services for example) should be quite secure. All test run in taint mode. Bio::Grep checks the settings before it generates the string for the system() call and uses File::Temp for all temporary files.

However, keep in mind that it is quite easy to start a query that will run forever without any further settings check, especially with the RE back-end. So you should limit mismatches, query_length and all other settings that have an significant impact on the calculation time. You should also set maxhits.

INCOMPATIBILITIES

None reported.

BUGS AND LIMITATIONS

No bugs have been reported.

There is not yet a nice interface for searching for multiple queries. However, Vmatch and GUUGle support this feature. So you can generate a Fasta query file with Bio::SeqIO and then set $sbe->settings->query_file(). To find out, to which query a match belongs, you have to check $res->query.

It is likely that $sbe->settings->query is renamed to queries().

Please report any bugs or feature requests to bug-bio-grep@rt.cpan.org, or through the web interface at http://rt.cpan.org.

SEE ALSO

Bio::Grep::Cookbook Bio::Grep::Backend::BackendI Bio::Grep::Backend::Vmatch Bio::Grep::Backend::GUUGle Bio::Grep::Backend::RE Bio::Grep::Backend::Agrep Bio::Grep::Benchmarks

PUBLICATIONS

GUUGle: http://bioinformatics.oxfordjournals.org/cgi/content/full/22/6/762

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.