Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s) use strict; use Bio::Index::Blast; my ($indexfile,$file1, $file2); my $index = new Bio::Index::Blast(-filename => $indexfile, -write_flag => 1); $index->make_index($file1, $file2); my $id; my $data = $index->get_stream($id); my $bplite_report = $index->fetch_report($id); print "query is ", $bplite_report->query, "\n"; while( my $sbjct = $bplite_report->nextSbjct ) { print $sbjct->name, "\n"; while( my $hsp = $sbjct->nextHSP ) { print "\t e-value ", $hsp->P, } print "\n"; } This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. Note: for best results 'use strict'.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email jason@cgt.mc.duke.edu Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Usage : $index = Bio::Index::Abstract->new( -filename => $dbm_file, -write_flag => 0, -dbm_package => 'DB_File', -verbose => 0); Function: Returns a new index object. If filename is specified, then open_dbm() is immediately called. Bio::Index::Abstract->new() will usually be called directly only when opening an existing index. Returns : A new index object Args : -filename The name of the dbm index file. -write_flag TRUE if write access to the dbm file is needed. -dbm_package The Perl dbm module to use for the index. -verbose Print debugging output to STDERR if TRUE.

Bio::Index::Blast implemented methods

fetch_report
Title : fetch_report Usage : my $blastreport = $idx->fetch_report($id); Function: Returns a Bio::Search::Result::ResultI report object for a specific blast report Returns : Bio::Search::Result::ResultI Args : valid id

id_parser
Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Useful for (for instance) specifying a different parser for different flavours of blast dbs. Returns \&default_id_parser (see below) if not set. If you supply your own id_parser subroutine, then it should expect a fasta description line. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE

default_id_parser
Title : default_id_parser Usage : $id = default_id_parser( $header ) Function: The default Blast Query ID parser for Bio::Index::Blast.pm Returns $1 from applying the regexp /^>\s*(\S+)/ to $header. Returns : ID string Args : a header line string

Require methods from Bio::Index::Abstract

_index_file
Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index BLAST report file(s). Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args :

filename
Title : filename Usage : $value = $self->filename(); $self->filename($value); Function: Gets or sets the name of the dbm index file. Returns : The current value of filename Args : Value of filename if setting, or none if getting the value.

write_flag
Title : write_flag Usage : $value = $self->write_flag(); $self->write_flag($value); Function: Gets or sets the value of write_flag, which is wether the dbm file should be opened with write access. Returns : The current value of write_flag (default 0) Args : Value of write_flag if setting, or none if getting the value.

dbm_package
Usage : $value = $self->dbm_package(); $self->dbm_package($value); Function: Gets or sets the name of the Perl dbm module used. If the value is unset, then it returns the value of the package variable $USE_DBM_TYPE or if that is unset, then it chooses the best available dbm type, choosing 'DB_File' in preference to 'SDBM_File'. Bio::Abstract::Index may work with other dbm file types. Returns : The current value of dbm_package Args : Value of dbm_package if setting, or none if getting the value.

get_stream
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

open_dbm
Usage : $index->open_dbm() Function: Opens the dbm file associated with the index object. Write access is only given if explicitly asked for by calling new(-write => 1) or having set the write_flag(1) on the index object. The type of dbm file opened is that returned by dbm_package(). The name of the file to be is opened is obtained by calling the filename() method. Example : $index->_open_dbm() Returns : 1 on success

_version
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

_filename
Title : _filename Usage : $index->_filename( FILE INT ) Function: Indexes the file Example : Returns : Args :

_file_handle
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

_file_count
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 : INT Args : INT

add_record
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. If $id is a reference to an array, then a new entry is added under a key corresponding to each element of the array. Example : $index->add_record( $id, $fileNumber, $begin, $end ) Returns : TRUE on success or FALSE on failure Args : ID LIST

pack_record
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

unpack_record
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

DESTROY
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