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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 - [email protected]CONTRIBUTORS
Jason Stajich, [email protected]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)