Bio::DB::Flat::BinarySearch(3pm)

NAME
Bio::DB::Flat::BinarySearch - BinarySearch search indexing system for sequence files

SYNOPSIS
  TODO: SYNOPSIS NEEDED!

DESCRIPTION
This module can be used both to index sequence files and also to retrieve sequences from existing sequence files.

This object allows indexing of sequence files both by a primary key (say accession) and multiple secondary keys (say ids). This is different from the Bio::Index::Abstract (see Bio::Index::Abstract) which uses DBM files as storage. This module uses a binary search to retrieve sequences which is more efficient for large datasets.

  Index creation
    my $sequencefile;  # Some fasta sequence file

Patterns have to be entered to define where the keys are to be indexed and also where the start of each record. E.g. for fasta

    my $start_pattern   = '^>';
    my $primary_pattern = '^>(\S+)';

So the start of a record is a line starting with a > and the primary key is all characters up to the first space after the >

A string also has to be entered to defined what the primary key (primary_namespace) is called.

The index can now be created using

    my $index = Bio::DB::Flat::BinarySearch->new(
             -directory         => "/home/max/",
             -dbname            => "mydb",
              -start_pattern     => $start_pattern,
              -primary_pattern   => $primary_pattern,
             -primary_namespace => "ID",
              -format            => "fasta" );

    my @files = ("file1","file2","file3");

    $index->build_index(@files);

The index is now ready to use. For large sequence files the perl way of indexing takes a *long* time and a *huge* amount of memory. For indexing things like dbEST I recommend using the DB_File indexer, BDB.

The formats currently supported by this module are fasta, Swissprot, and EMBL.

  Creating indices with secondary keys
Sometimes just indexing files with one id per entry is not enough. For instance you may want to retrieve sequences from swissprot using their accessions as well as their ids.

To be able to do this when creating your index you need to pass in a hash of secondary_patterns which have their namespaces as the keys to the hash.

e.g. For Indexing something like

ID 1433_CAEEL STANDARD; PRT; 248 AA. AC P41932; DT 01-NOV-1995 (Rel. 32, Created) DT 01-NOV-1995 (Rel. 32, Last sequence update) DT 15-DEC-1998 (Rel. 37, Last annotation update) DE 14-3-3-LIKE PROTEIN 1. GN FTT-1 OR M117.2. OS Caenorhabditis elegans. OC Eukaryota; Metazoa; Nematoda; Chromadorea; Rhabditida; Rhabditoidea; OC Rhabditidae; Peloderinae; Caenorhabditis. OX NCBI_TaxID=6239; RN [1]

where we want to index the accession (P41932) as the primary key and the id (1433_CAEEL) as the secondary id. The index is created as follows

    my %secondary_patterns;

    my $start_pattern   = '^ID   (\S+)';
    my $primary_pattern = '^AC   (\S+)\;';

    $secondary_patterns{"ID"} = '^ID   (\S+)';

    my $index = Bio::DB::Flat::BinarySearch->new(
                -directory          => $index_directory,
                  -dbname             => "ppp",
                  -write_flag         => 1,
                -verbose            => 1,
                -start_pattern      => $start_pattern,
                -primary_pattern    => $primary_pattern,
                -primary_namespace  => 'AC',
                -secondary_patterns => \%secondary_patterns);

    $index->build_index($seqfile);

Of course having secondary indices makes indexing slower and use more memory.

  Index reading
To fetch sequences using an existing index first of all create your sequence object

    my $index = Bio::DB::Flat::BinarySearch->new(
                  -directory => $index_directory);

Now you can happily fetch sequences either by the primary key or by the secondary keys.

    my $entry = $index->get_entry_by_id('HBA_HUMAN');

This returns just a string containing the whole entry. This is useful is you just want to print the sequence to screen or write it to a file.

Other ways of getting sequences are

    my $fh = $index->get_stream_by_id('HBA_HUMAN');

This can then be passed to a seqio object for output or converting into objects.

    my $seq = Bio::SeqIO->new(-fh     => $fh,
                                -format => 'fasta');

The last way is to retrieve a sequence directly. This is the slowest way of extracting as the sequence objects need to be made.

    my $seq = $index->get_Seq_by_id('HBA_HUMAN');

To access the secondary indices the secondary namespace needs to be known

    $index->secondary_namespaces("ID");

Then the following call can be used

    my $seq   = $index->get_Seq_by_secondary('ID','1433_CAEEL');

These calls are not yet implemented

    my $fh    = $index->get_stream_by_secondary('ID','1433_CAEEL');
    my $entry = $index->get_entry_by_secondary('ID','1433_CAEEL');

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Michele Clamp
Email - michele@sanger.ac.uk

CONTRIBUTORS
Jason Stajich, jason@bioperl.org

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).

  new
 Title   : new
 Usage   : For reading
             my $index = Bio::DB::Flat::BinarySearch->new(
                     -directory => '/Users/michele/indices/dbest',
             -dbname    => 'mydb',
                     -format    => 'fasta');

           For writing

             my %secondary_patterns = {"ACC" => "^>\\S+ +(\\S+)"}
             my $index = Bio::DB::Flat::BinarySearch->new(
             -directory          => '/Users/michele/indices',
                     -dbname             => 'mydb',
             -primary_pattern    => "^>(\\S+)",
                     -secondary_patterns => \%secondary_patterns,
             -primary_namespace  => "ID");

             my @files = ('file1','file2','file3');

             $index->build_index(@files);

 Function: create a new Bio::DB::Flat::BinarySearch object
 Returns : new Bio::DB::Flat::BinarySearch
 Args    : -directory          Root directory for index files
           -dbname             Name of subdirectory containing indices
                               for named database
           -write_flag         Allow building index
           -primary_pattern    Regexp defining the primary id
           -secondary_patterns A hash ref containing the secondary
                               patterns with the namespaces as keys
           -primary_namespace  A string defining what the primary key
                               is

 Status  : Public

  get_Seq_by_id
 Title   : get_Seq_by_id
 Usage   : $obj->get_Seq_by_id($newval)
 Function:
 Example :
 Returns : value of get_Seq_by_id
 Args    : newvalue (optional)

  get_entry_by_id
 Title   : get_entry_by_id
 Usage   : $obj->get_entry_by_id($newval)
 Function: Get a Bio::SeqI object for a unique ID
 Returns : Bio::SeqI
 Args    : string

  get_stream_by_id
 Title   : get_stream_by_id
 Usage   : $obj->get_stream_by_id($id)
 Function: Gets a Sequence stream for an id
 Returns : Bio::SeqIO stream
 Args    : Id to lookup by

  get_Seq_by_acc
 Title   : get_Seq_by_acc
 Usage   : $obj->get_Seq_by_acc($acc)
 Function: Gets a Bio::SeqI object by accession number
 Returns : Bio::SeqI object
 Args    : string representing accession number

  get_Seq_by_version
 Title   : get_Seq_by_version
 Usage   : $obj->get_Seq_by_version($version)
 Function: Gets a Bio::SeqI object by accession.version number
 Returns : Bio::SeqI object
 Args    : string representing accession.version number

  get_Seq_by_secondary
 Title   : get_Seq_by_secondary
 Usage   : $obj->get_Seq_by_secondary($namespace,$acc)
 Function: Gets a Bio::SeqI object looking up secondary accessions
 Returns : Bio::SeqI object
 Args    : namespace name to check secondary namespace and an id

  read_header
 Title   : read_header
 Usage   : $obj->read_header($fhl)
 Function: Reads the header from the db file
 Returns : width of a record
 Args    : filehandle

  read_record
 Title   : read_record
 Usage   : $obj->read_record($fh,$pos,$len)
 Function: Reads a record from a filehandle
 Returns : String
 Args    : filehandle, offset, and length

  get_all_primary_ids
 Title   : get_all_primary_ids
 Usage   : @ids = $seqdb->get_all_primary_ids()
 Function: gives an array of all the primary_ids of the
           sequence objects in the database.
 Returns : an array of strings
 Args    : none

  find_entry
 Title   : find_entry
 Usage   : $obj->find_entry($fh,$start,$end,$id,$recsize)
 Function: Extract an entry based on the start,end,id and record size
 Returns : string
 Args    : filehandle, start, end, id, recordsize

  build_index
 Title   : build_index
 Usage   : $obj->build_index(@files)
 Function: Build the index based on a set of files
 Returns : count of the number of entries
 Args    : List of filenames

  _index_file
 Title   : _index_file
 Usage   : $obj->_index_file($newval)
 Function:
 Example :
 Returns : value of _index_file
 Args    : newvalue (optional)

  write_primary_index
 Title   : write_primary_index
 Usage   : $obj->write_primary_index($newval)
 Function:
 Example :
 Returns : value of write_primary_index
 Args    : newvalue (optional)

  write_secondary_indices
 Title   : write_secondary_indices
 Usage   : $obj->write_secondary_indices($newval)
 Function:
 Example :
 Returns : value of write_secondary_indices
 Args    : newvalue (optional)

  new_secondary_filehandle
 Title   : new_secondary_filehandle
 Usage   : $obj->new_secondary_filehandle($newval)
 Function:
 Example :
 Returns : value of new_secondary_filehandle
 Args    : newvalue (optional)

  open_secondary_index
 Title   : open_secondary_index
 Usage   : $obj->open_secondary_index($newval)
 Function:
 Example :
 Returns : value of open_secondary_index
 Args    : newvalue (optional)

  _add_id_position
 Title   : _add_id_position
 Usage   : $obj->_add_id_position($newval)
 Function:
 Example :
 Returns : value of _add_id_position
 Args    : newvalue (optional)

  make_config_file
 Title   : make_config_file
 Usage   : $obj->make_config_file($newval)
 Function:
 Example :
 Returns : value of make_config_file
 Args    : newvalue (optional)

  read_config_file
 Title   : read_config_file
 Usage   : $obj->read_config_file($newval)
 Function:
 Example :
 Returns : value of read_config_file
 Args    : newvalue (optional)

  get_fileid_by_filename
 Title   : get_fileid_by_filename
 Usage   : $obj->get_fileid_by_filename($newval)
 Function:
 Example :
 Returns : value of get_fileid_by_filename
 Args    : newvalue (optional)

  get_filehandle_by_fileid
 Title   : get_filehandle_by_fileid
 Usage   : $obj->get_filehandle_by_fileid($newval)
 Function:
 Example :
 Returns : value of get_filehandle_by_fileid
 Args    : newvalue (optional)

  primary_index_file
 Title   : primary_index_file
 Usage   : $obj->primary_index_file($newval)
 Function:
 Example :
 Returns : value of primary_index_file
 Args    : newvalue (optional)

  primary_index_filehandle
 Title   : primary_index_filehandle
 Usage   : $obj->primary_index_filehandle($newval)
 Function:
 Example :
 Returns : value of primary_index_filehandle
 Args    : newvalue (optional)

  format
 Title   : format
 Usage   : $obj->format($newval)
 Function:
 Example :
 Returns : value of format
 Args    : newvalue (optional)

  write_flag
 Title   : write_flag
 Usage   : $obj->write_flag($newval)
 Function:
 Example :
 Returns : value of write_flag
 Args    : newvalue (optional)

  dbname
 Title   : dbname
 Usage   : $obj->dbname($newval)
 Function: get/set database name
 Example :
 Returns : value of dbname
 Args    : newvalue (optional)

  index_directory
 Title   : index_directory
 Usage   : $obj->index_directory($newval)
 Function:
 Example :
 Returns : value of index_directory
 Args    : newvalue (optional)

  record_size
 Title   : record_size
 Usage   : $obj->record_size($newval)
 Function:
 Example :
 Returns : value of record_size
 Args    : newvalue (optional)

  primary_namespace
 Title   : primary_namespace
 Usage   : $obj->primary_namespace($newval)
 Function:
 Example :
 Returns : value of primary_namespace
 Args    : newvalue (optional)

  index_type
 Title   : index_type
 Usage   : $obj->index_type($newval)
 Function:
 Example :
 Returns : value of index_type
 Args    : newvalue (optional)

  index_version
 Title   : index_version
 Usage   : $obj->index_version($newval)
 Function:
 Example :
 Returns : value of index_version
 Args    : newvalue (optional)

  primary_pattern
 Title   : primary_pattern
 Usage   : $obj->primary_pattern($newval)
 Function:
 Example :
 Returns : value of primary_pattern
 Args    : newvalue (optional)

  start_pattern
 Title   : start_pattern
 Usage   : $obj->start_pattern($newval)
 Function:
 Example :
 Returns : value of start_pattern
 Args    : newvalue (optional)

  secondary_patterns
 Title   : secondary_patterns
 Usage   : $obj->secondary_patterns($newval)
 Function:
 Example :
 Returns : value of secondary_patterns
 Args    : newvalue (optional)

  secondary_namespaces
 Title   : secondary_namespaces
 Usage   : $obj->secondary_namespaces($newval)
 Function:
 Example :
 Returns : value of secondary_namespaces
 Args    : newvalue (optional)