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BioPerl-1.6.924
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/ Bio::DB::Flat::BinarySearch

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)