Provided by: libbio-perl-perl_1.6.901-2_all bug

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://redmine.open-bio.org/projects/bioperl/

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)