Ewan Birney

NAME

Bio::DB::Flat::OBDAIndex - Binary search indexing system for sequence files

SYNOPSIS

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

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 afterf 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 = new Bio::DB::Flat::OBDAIndex(
             -start_pattern   => $start_pattern,
             -primary_pattern => $primary_pattern,
             -primary_namespace => "ACC",
                                             );

To actually write it out to disk we need to enter a directory where the indices will live, a database name and an array of sequence files to index.

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

    $index->make_index("/Users/michele/indices","mydatabase",@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 C indexer.

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 = new Bio::DB::Flat::OBDAIndex(
                -start_pattern     => $start_pattern,
                -primary_pattern   => $primary_pattern,
                -primary_namespace  => 'ACC',
                -secondary_patterns => \%secondary_patterns);

    $index->make_index("/Users/michele/indices","mydb",($seqfile));

Of course having secondary indices makes indexing slower and more of a memory hog.

Index reading

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

    my $index = new Bio::DB::Flat::OBDAIndex(-index_dir => $index_directory,
                                             -dbname    => 'swissprot');

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 = new Bio::SeqIO(-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 (use $index->secondary_namespaces) and the following call used

    my $seq   = $index->get_Seq_by_secondary('ACC','Q21973');
    my $fh    = $index->get_stream_by_secondary('ACC','Q21973');
    my $entry = $index->get_entry_by_secondary('ACC','Q21973');

DESCRIPTION

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.

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/MailList.shtml - About the mailing lists

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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Michele Clamp

Email - michele@sanger.ac.uk

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 = new Bio::DB::Flat::OBDAIndex(
                     -index_dir => '/Users/michele/indices/',
                     -dbname    => 'dbEST',
                     -format    => 'fasta');

           For writing 

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

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

             $index->make_index('mydbname',@files);    


 Function: create a new Bio::DB::Flat::OBDAIndex object
 Returns : new Bio::DB::Flat::OBDAIndex
 Args    : -index_dir          Directory containing the indices
           -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: 
 Example : 
 Returns : 
 Args    : 

get_stream_by_id

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

get_Seq_by_acc

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

get_Seq_by_secondary

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

read_header

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

read_record

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

find_entry

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

make_index

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

_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_indexdir

 Title   : make_indexdir
 Usage   : $obj->make_indexdir($newval)
 Function: 
 Example : 
 Returns : value of make_indexdir
 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)

database_name

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

format

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