NAME

Bio::Grep::Backend::BackendI - Superclass for all back-ends

SYNOPSIS

See the back-end modules for example code.

DESCRIPTION

Bio::Grep::Backend::BackendI is the superclass for all back-ends. Don't use this class directly.

METHODS

See Bio::Grep::Root for inherited methods.

new()

This method constructs a Bio::Grep::Backend::BackendI object and is never used directly. Rather, all other back-ends in this package inherit the methods of this interface and call its constructor internally.

$sbe->next_res

Returns next result as a Bio::Grep::SearchResult object after search() was called.

    $sbe->search();

    while ( my $res = $sbe->next_res ) {
        # output result
    }
$sbe->results()

Get the results after search() was called. This is an array of Bio::Grep::SearchResult objects.

  $sbe->search();

  foreach my $res (@{$sbe->results}) {
        # output result
  }

This method is DEPRECATED. See next_res().

$sbe->settings()

Get the settings. This is a Bio::Grep::SearchSettings object

  # search for the reverse complement and allow 4 mismatches
  $sbe->settings->database('ATH1.cdna');
  $sbe->settings->query('UGAACAGAAAGCUCAUGAGCC');
  $sbe->settings->reverse_complement(1);
  $sbe->settings->mismatches(4);
$sbe->features()

Get available features. This is a hash. Valid features are MISMATCHES, GUMISMATCHES, EDITDISTANCE, INSERTIONS, DELETIONS, FILTERS, NATIVE_ALIGNMENTS, PROTEINS, UPSTREAM, DOWNSTREAM, MAXHITS, COMPLETE, QUERY, QUERY_FILE, QUERY_LENGTH, DIRECT_AND_REV_COM, SHOWDESC, QSPEEDUP, HXDROP, EXDROP, EVALUE and PERCENT_IDENTITY.

  if (defined($sbe->features->{GUMISMATCHES})) {
          # $sbe->settings->gumismatches(0);
          $sbe->settings->gumismatches(0.5);
  } else {
        print "\nBack-end does not support wobble pairs\n";
  }
$sbe->get_alphabet_of_database($db)

Returns 'dna' if the specified database is a DNA database, 'protein' otherwise.

ABSTRACT METHODS

Every back-end must implement these methods.

$sbe->search

This method starts the back-end with the settings specified in the Bio::Grep::SearchSettings object $sbe->settings.

    $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 => $query });
$sbe->get_sequences

This method returns all sequences with the ids in the specified array reference as a Bio::SeqIO object.

   my $seqio = $sbe->get_sequences([$id]);
   my $string;  my $stringio = IO::String->new($string);
   my $out = Bio::SeqIO->new('-fh' => $stringio,
                             '-format' => 'fasta');

   while ( my $seq = $seqio->next_seq() ) {
      # write the sequences in a string
      $out->write_seq($seq);
   }
   print $string;
 
$sbe->get_databases

Returns a hash with all available databases. The keys are the filenames, the values are descriptions (or the filename if no description is available).

Descriptions can be set in info files. For example, if you indexed file ATH1.cdna, Vmatch and HyPA construct a lot of ATH1.cdna.* files. Now simply create a file ATH1.cdna.nfo and write a description in that file. The method generate_database() will create this file for you if you add a description as second argument.

  my %local_dbs_description = $sbe->get_databases();
  my @local_dbs = sort keys %local_dbs_description;
  
  # take first available database 
  $sbe->settings->database($local_dbs[0]);
$sbe->generate_database($fastafile)

Copies the specified Fasta file in the datapath directory ($sbe->settings->datapath) and generates a database (HyPa/Vmatch: a suffix array). You can get the available databases with $sbe->get_databases(). You have to do this only once. Vmatch and HyPa need a lot of RAM for the construction of their enhanced suffix arrays.

  $sbe->generate_database('ATH1.cdna', 'AGI Transcripts');
$sbe->generate_database_out_of_fastafile($fastafile)

DEPRECATED. Use generate_database() instead.

$sbe->available_sort_modes()

Returns a hash with the available result sort modes. Keys are the modes you can set with $sbe->settings->sort($mode), values a short description.

INTERNAL METHODS

Only back-ends should call them directly.

_check_search_settings

Performs some basic error checking. Important security checks, because we use system(). So we should check, if we get what we assume.

Because every back-end should call this method at the top of its search method, we clean things like old search results here up.

_prepare_query

Another important method that every back-end must call. Prepares the query, for example calculating the reverse complement if necessary, returns the prepared query. settings->query is unchanged!

_copy_fasta_file_and_create_nfo

The generate_database() implementation of your back-end class should use this method to copy the specified Fasta file to the data directory and to generate an info file, containing the description of the Fasta file.

_get_alignment( $seq_query, $seq_subject )

Calculates and returns an alignment of two Bio::Seq objects. Requires EMBOSS and bioperl-run.

_get_databases($suffix)

This method searches the data directory for files ending with $suffix and returns this list of files in an array.

Substitutes $suffix with .nfo from all found files and searches for an info file with that name. The content of that file will be used as description. When no file is found, the description will be the filename without the suffix:

   %dbs = _get_databases('.al1');  # finds file ATH1.cdna.al1, searches for
                                   # ATH1.cdna.nfo
   print $dbs{'ATH1.cdna'};        # prints content of ATH1.cdna.nfo or 
                                   # 'ATH1.cdna'
_get_sequences_from_bio_index($id)

GUUGle, Hypa, RE and Agrep back-ends use Bio::Index for sequence id queries (implemented in this this method). Returns a Bio::SeqIO object like abstract method get_sequences() should.

_create_tmp_query_file()

Examines query, query_file and reverse_complement and generates a temporary Fasta file that is passed in the system() call to the backend. If the environment variable BIOGREPDEBUG is not set, then this file will be deleted when the script exits.

_create_index_and_alphabet_file($fastafile)

Creates an index of the specified Fasta file with Bio::Index::Fasta. Creates an Vmatch alphabet file.

DIAGNOSTICS

See Bio::Grep::Root for other diagnostics.

Alphabet of query and database not equal

You tried to search with DNA/RNA query in protein database or vice versa. Bio::Root::BadParameter.

Back-end does not support protein data

You tried to generate a protein database with a back-end that does not support protein data. Bio::Root::BadParameter.

Can't combine editdistance and mismatches.

Set either editdistance or mismatches, not both. Bio::Root::BadParameter

Can't copy ... to ...

It was not possible to copy the Fasta file in generate_database() in the data directory. Check path and permissions. Bio::Root::IOException.

Database not defined.

You forgot to define a database. You have to build a database with $sbe->generate_database (once) and set it with $sbe->settings->database. Example:

  $sbe->generate_database('ATH1.cdna");
  $sbe->settings->database('ATH1.cdna');

Bio::Root::BadParameter.

Database not found.

The specified database was not found. Check name and $sbe->settings->datapath. Bio::Root::BadParameter.

Database not valid (insecure characters).

The database name is not valid. Allowed characters are 'a-z', 'A-z','0-9', '.' , '-' and '_'. Bio::Root::BadParameter.

Query and query_file are set. I am confused...

You specified a query and a query file. Bio::Root::BadParameter.

Query not defined.

You forgot to define a query or a query file. Bio::Root::BadParameter.

Sort mode not valid.

The specified sort mode ($sbe->settings->sort) is not valid. You can get all valid sort modes with $sbe->available_sort_modes() See Bio::Grep::Backend::Vmatch, Bio::Grep::Backend::Hypa, Bio::Grep::Backend::Agrep for details. Bio::Root::BadParameter.

FILES

Requires EMBOSS and Bio::Factory::EMBOSS for the Needleman-Wunsch local alignment implementation from EMBOSS. The internal method _get_alignment($seq_a, $seq_b) can than calculate an alignment for back-ends that do not generate a alignment (like Bio::Grep::Backend::Hypa or Bio::Grep::Backend::Agrep).

SEE ALSO

Bio::Grep::SearchSettings Bio::Grep::SearchResults

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.

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