Bio::Index::Abstract - Abstract interface for indexing a flat file
You should not be using this module directly
To use DB_FILE and not SDBM for this index, do the following
$Bio::Index::Abstract::USE_DBM_TYPE = 'DB_File';
This object provides the basic mechanism to associate positions in files with names. The position and filenames are stored in DBM which can then be accessed later on. It is the equivalent of flat file indexing (eg, SRS or efetch).
This object is the guts to the mechanism, which will be used by the specific objects inheriting from it.
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.
vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists
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 - birney@sanger.ac.uk, jgrg@sanger.ac.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with an "_" (underscore).
Title : _initialize Usage : $index->_initialize Function: Initializes data structures in the index object, opens or creates the dbm file, and performs a number of pre-flight checks, which depend on the existance of certain methods in the sub class. In particular the sub class should provide the _version() and _type() methods (see below). Example : $index->SUPER::_initialize # add this call to the # sub class's _initialize() # function if the sub # class needs to do its # own initializing Returns : Args :
Title : filename Usage : $name = $index->filename() Function: Returns the name of the index file Example : Returns : STRING Args : NONE
Title : db Usage : $index->db Function: Returns a ref to the hash which is tied to the dbm file. Used internally when adding and retrieving data from the database. Example : $db = $index->db(); $db->{ $some_key } = $data $data = $index->db->{ $some_key }; Returns : ref to HASH Args : NONE
Title : get_stream Usage : $stream = $index->get_stream( $id ); Function: Returns a file handle with the file pointer at the approprite place This provides for a way to get the actual file contents and not an object WARNING: you must parse the record deliminter *yourself*. Abstract wont do this for you So this code $fh = $index->get_stream($myid); while( <$fh> ) { # do something } will parse the entire file if you don't put in a last statement in, like while( <$fh> ) { /^\/\// && last; # end of record # do something } Returns : A filehandle object Args : string represents the accession number Notes : This method should not be used without forethought
Title : _open_dbm Usage : $index->_open_dbm() Function: Called by _initialize() to create or open an existing index dbm file for adding and retieving records. Write access is only given if explicitly asked for by passing the string 'WRITE' as the second argument to the new() function (which calls initialize). The type of dbm file opened, DB_File or SDBM_File, depends upon wether the global variable $USE_DBM_TYPE is set to 'DB_File' or 'SDBM_File' respectively. The name of the file to be is opened is obtained by calling the filename() method. Example : $index->_open_dbm('WRITE') Returns : 1 on success Args : 'WRITE' - optional
Title : _version Usage : $type = $index->_version() Function: Returns a string which identifes the version of an index module. Used to permanently identify an index file as having been created by a particular version of the index module. Must be provided by the sub class Example : Returns : Args : none
Title : _code_base Usage : $code = $db->_code_base(); Function: Example : Returns : Code package to be used with this Args :
Title : _type_and_version Usage : Called by _initalize Function: Checks that the index opened is made by the same index module and version of that module that made it. If the index is empty, then it adds the information to the database. Example : Returns : 1 or exception Args : none
Title : _check_file_sizes Usage : $index->_check_file_sizes() Function: Verifies that the files listed in the database are the same size as when the database was built, or throws an exception. Called by the _initialize() function. Example : Returns : 1 or exception Args :
Title : make_index Usage : $index->make_index( FILE_LIST ) Function: Takes a list of file names, checks that they are all fully qualified, and then calls _index_file() on each. It supplies _index_file() with the name of the file, and an integer which is stored with each record created by _index_file(). Can be called multiple times, and can be used to add to an existing index file. Example : $index->make_index( '/home/seqs1', '/home/seqs2', '/nfs/pub/big_db' ); Returns : Number of files indexed Args : LIST OF FILES
Title : _index_file Usage : $index->_index_file( FILE INT ) Function: Indexes the file Example : Returns : Args :
Title : _file_handle Usage : $fh = $index->_file_handle( INT ) Function: Returns an open filehandle for the file index INT. On opening a new filehandle it caches it in the @{$index->_filehandle} array. If the requested filehandle is already open, it simply returns it from the array. Example : $fist_file_indexed = $index->_file_handle( 0 ); Returns : ref to a filehandle Args : INT
Title : _file_count Usage : $index->_file_count( INT ) Function: Used by the index building sub in a sub class to track the number of files indexed. Sets or gets the number of files indexed when called with or without an argument. Example : Returns : Args : INT
Title : add_record Usage : $index->add_record( $id, @stuff ); Function: Calls pack_record on @stuff, and adds the result of pack_record to the index database under key $id. Example : $index->add_record( $id, $fileNumber, $begin, $end ) Returns : TRUE on success or FALSE on failure Args : ID LIST
Title : pack_record Usage : $packed_string = $index->pack_record( LIST ) Function: Packs an array of scalars into a single string joined by ASCII 034 (which is unlikely to be used in any of the strings), and returns it. Example : $packed_string = $index->pack_record( $fileNumber, $begin, $end ) Returns : STRING or undef Args : LIST
Title : unpack_record Usage : $index->unpack_record( STRING ) Function: Splits the sting provided into an array, splitting on ASCII 034. Example : ( $fileNumber, $begin, $end ) = $index->unpack_record( $self->db->{$id} ) Returns : A 3 element ARRAY Args : STRING containing ASCII 034
Title : verbose Usage : $obj->verbose($newval) Function: sets whether a report to STDERR should be issued or not for each sequence indexed. Helps track errors Example : Returns : value of verbose Args : newvalue (optional)
Title : DESTROY Usage : Called automatically when index goes out of scope Function: Closes connection to database and handles to sequence files Returns : NEVER Args : NONE
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.