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Bio::Index::Blast.3pm

NAME

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

SYNOPSIS

   use strict;
   use Bio::Index::Blast;
 
   my ($indexfile,$file1,$file2,$query);
   my $index = Bio::Index::Blast->new(-filename => $indexfile,
                                                          -write_flag => 1);
   $index->make_index($file1,$file2);
 
   my $fh = $index->get_stream($query);
 
   my $blast_report = Bio::SearchIO->new(-noclose => 1,
                                         -format  => 'blast',
                                         -fh      => $fh);
   my $result = $blast_report->next_result;
   print $result->algorithm, "\n";
   my $hit = $result->next_hit;
   print $hit->description, "\n";
   my $hsp = $hit->next_hsp;
   print $hsp->bits, "\n";
 
 

DESCRIPTION

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.

This also allows for ID parsing using a callback:

    $inx->id_parser(\&get_id);
    # make the index
    $inx->make_index($file_name);
 
    # here is where the retrieval key is specified
    sub get_id {
       my $line = shift;
       $line =~ /^>.+gi\|(\d+)/;
       $1;
    }
 
 

The indexer is capable of indexing based on multiple IDs passed back from the callback; this is assuming of course all IDs are unique.

Note: for best results 'use strict'.

FEEDBACK

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/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

APPENDIX

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::SearchIO report object 
            for a specific blast report
  Returns : Bio::SearchIO
  Args    : valid id
 
 

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    :
 
 

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
 
 

Bio::Index::Abstract methods

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 do not 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