Raw content of Bio::Index::Blast
<![CDATA[# $Id: Blast.pm,v 1.8.2.1 2003/06/28 21:57:04 jason Exp $
#
# BioPerl module for Bio::Index::Blast
#
# Cared for by Jason Stajich <jason@cgt.mc.duke.edu>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Index::Blast - Indexes Blast reports and supports retrieval based on query accession(s)
=head1 SYNOPSIS
use strict;
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";
}
=head1 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.
Note: for best results 'use strict'.
=head1 FEEDBACK
=head2 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
=head2 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/
=head1 AUTHOR - Jason Stajich
Email jason@cgt.mc.duke.edu
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Index::Blast;
use vars qw(@ISA $VERSION);
use strict;
use Bio::Root::Root;
use Bio::Index::Abstract;
use Bio::Tools::BPlite;
use IO::String;
@ISA = qw(Bio::Index::Abstract Bio::Root::Root );
BEGIN {
$VERSION = 0.1;
}
sub _version {
return $VERSION;
}
=head2 new
Usage : $index = Bio::Index::Abstract->new(
-filename => $dbm_file,
-write_flag => 0,
-dbm_package => 'DB_File',
-verbose => 0);
Function: Returns a new index object. If filename is
specified, then open_dbm() is immediately called.
Bio::Index::Abstract->new() will usually be called
directly only when opening an existing index.
Returns : A new index object
Args : -filename The name of the dbm index file.
-write_flag TRUE if write access to the dbm file is
needed.
-dbm_package The Perl dbm module to use for the
index.
-verbose Print debugging output to STDERR if
TRUE.
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
}
=head2 Bio::Index::Blast implemented methods
=cut
=head2 fetch_report
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
=cut
sub fetch_report{
my ($self,$id) = @_;
my $fh = $self->get_stream($id);
my $report = new Bio::Tools::BPlite(-fh => $fh,
-noclose => 1);
return $report;
}
# shamlessly stolen from Bio::Index::Fasta
=head2 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
=cut
sub id_parser {
my( $self, $code ) = @_;
if ($code) {
$self->{'_id_parser'} = $code;
}
return $self->{'_id_parser'} || \&default_id_parser;
}
=head2 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 $header.
Returns : ID string
Args : a header line string
=cut
sub default_id_parser {
if ($_[0] =~ /^\s*(\S+)/) {
return $1;
} else {
return;
}
}
=head2 Require methods from Bio::Index::Abstract
=cut
=head2 _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 :
=cut
sub _index_file {
my( $self,
$file, # File name
$i, # Index-number of file being indexed
) = @_;
my( $begin, # Offset from start of file of the start
# of the last found record.
);
open(BLAST, "<$file") or die("cannot open file $file\n");
my (@data, @records);
my $indexpoint = 0;
my $lastline = 0;
while(<BLAST> ) {
if( /(T)?BLAST[PNX]/ ) {
if( @data ) {
# if we have already read a report
# then store the data for this report
# in the CURRENT index
$self->_process_report($indexpoint, $i,join("",@data));
} # handle fencepost problem (beginning)
# by skipping here when empty
# since we are at the beginning of a new report
# store this begin location for the next index
$indexpoint = $lastline;
@data = ();
}
push @data, $_;
$lastline = tell(BLAST);
}
# handle fencepost problem (end)
if( @data ) {
$self->_process_report($indexpoint,$i,join("",@data));
}
}
sub _process_report {
my ($self,$begin,$i,$data) = @_;
if( ! $data ) {
$self->warn("calling _process_report without a valid data string");
return ;
}
my $id_parser = $self->id_parser;
my $datal = new IO::String($data);
my $report = new Bio::Tools::BPlite(-fh => $datal,
-noclose => 1);
my $query = $report->query;
foreach my $id (&$id_parser($query)) {
print "id is $id, begin is $begin\n" if( $self->verbose > 0);
$self->add_record($id, $i, $begin);
}
}
=head2 Bio::Index::Abstract methods
=head2 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.
=head2 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.
=head2 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.
=head2 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
=head2 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
=head2 _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
=head2 _filename
Title : _filename
Usage : $index->_filename( FILE INT )
Function: Indexes the file
Example :
Returns :
Args :
=head2 _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
=head2 _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
=head2 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
=head2 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
=head2 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
=head2 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
=cut
1;
1;
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