--- name: "Bio::DB::Flat::OBDAIndex" section: "3pm" platform: "linux" package: "bioperl" version: "1.0-1" release: "Debian 3.0 (Woody)" platforms: ["linux"] url: "https://new.carta.tech/Bio::DB::Flat::OBDAIndex" --- # Bio::DB::Flat::OBDAIndex(3pm) Bio::DB::Flat::OBDAIndex - Binary search indexing system for sequence files 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'); ``` 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.\ **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/ ``` Email - michele@sanger.ac.uk 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) ``` **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) ```