Bio::DB::Flat - Interface for indexed flat files
$db = Bio::DB::Flat->new(-directory => '/usr/share/embl', -format => 'embl', -write_flag => 1); $db->build_index('/usr/share/embl/primate.embl','/usr/share/embl/protists.embl'); $seq = $db->get_Seq_by_id('BUM'); @sequences = $db->get_Seq_by_acc('DIV' => 'primate'); $raw = $db->fetch_raw('BUM');
This object provides the basic mechanism to associate positions in files with primary and secondary name spaces. Unlike Bio::Index::Abstract (see Bio::Index::Abstract), this is specialized to work with the "flat index" and BerkeleyDB indexed flat file formats worked out at the 2002 BioHackathon.
This object is a general front end to the underlying databases.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).
Title : new Usage : my $db = new Bio::Flat->new( -directory => $root_directory, -write_flag => 0, -index => 'bdb'|'flat', -verbose => 0, -out => 'outputfile', -format => 'genbank'); Function: create a new Bio::Index::BDB object Returns : new Bio::Index::BDB object Args : -directory Root directory containing "config.dat" -write_flag If true, allows reindexing. -verbose Verbose messages -out File to write to when write_seq invoked Status : Public
The root -directory indicates where the flat file indexes will be stored. The build_index() and write_seq() methods will automatically create a human-readable configuration file named "config.dat" in this file.
The -write_flag enables writing new entries into the database as well as the creation of the indexes. By default the indexes will be opened read only.
-index is one of "bdb" or "flat" and indicates the type of index to generate. "bdb" corresponds to Berkeley DB. You *must* be using BerkeleyDB version 2 or higher, and have the Perl BerkeleyDB extension installed (DB_File will *not* work).
The -out argument species the output file for writing objects created with write_seq().
Title : fetch Usage : $index->fetch( $id ) Function: Returns a Bio::Seq object from the index Example : $seq = $index->fetch( 'dJ67B12' ) Returns : Bio::Seq object Args : ID
Deprecated. Use get_Seq_by_id instead.
The following methods MUST be implemented by subclasses.
The following methods MAY be overridden by subclasses.
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.