Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)


    use Bio::Index::Blast;
    my $index = new Bio::Index::Blast(-filename => $indexfile,
                                      -write_flag => 1);
    $index->make_index($file1, $file2);

    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.


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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  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
            -dbm_package The Perl dbm module to use for the
            -verbose     Print debugging output to STDERR if

Bio::Index::Blast implemented methods


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


  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


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

Require methods from Bio::Index::Abstract


  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    : 

Bio::Index::Abstract methods


 Title   : filename
 Usage   : $value = $self->filename();
 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.


 Title   : write_flag
 Usage   : $value = $self->write_flag();
 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.


 Usage   : $value = $self->dbm_package();

 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

 Returns : The current value of dbm_package
 Args    : Value of dbm_package if setting, or none if
           getting the value.


 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 


  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


  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   : _filename
  Usage   : $index->_filename( 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 : INT
  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.
            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


  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   : DESTROY
 Usage   : Called automatically when index goes out of scope
 Function: Closes connection to database and handles to
           sequence files
 Returns : NEVER
 Args    : NONE