# $Id: blastxml.pm 16123 2009-09-17 12:57:27Z cjfields $
#
# BioPerl module for Bio::SearchIO::blastxml
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# 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::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
=head1 SYNOPSIS
use Bio::SearchIO;
my $searchin = Bio::SearchIO->new(-format => 'blastxml',
-file => 't/data/plague_yeast.bls.xml');
while( my $result = $searchin->next_result ) {
}
# one can also request that the parser NOT keep the XML data in memory
# by using the tempfile initialization flag.
my $searchin = Bio::SearchIO->new(-tempfile => 1,
-format => 'blastxml',
-file => 't/data/plague_yeast.bls.xml');
while( my $result = $searchin->next_result ) {
}
=head1 DESCRIPTION
This object implements a NCBI Blast XML parser. It requires XML::SAX; it is
also recommended (for faster parsing) that XML::SAX::ExpatXS or XML::LibXML
be installed. Either 'XML::SAX::ExpatXS' or 'XML::LibXML::SAX::Parser' should
be set as the default parser in ParserDetails.ini. This file is located in the
SAX subdirectory of XML in your local perl library (normally in the 'site'
directory).
Currently, XML::SAX::Expat will not work and will not be supported.
There is one additional initialization flag from the SearchIO defaults-
that is the -tempfile flag. If specified as true, then the parser
will write out each report to a temporary filehandle rather than
holding the entire report as a string in memory. The reason this is
done in the first place is NCBI reports have an uncessary E<lt>?xml
version="1.0"?E<gt> at the beginning of each report and RPS-BLAST reports
have an additional unecessary RPS-BLAST tag at the top of each report.
So we currently have implemented the work around by preparsing the
file (yes it makes the process slower, but it works).
=head1 DEPENDENCIES
In addition to parts of the Bio:: hierarchy, this module uses:
XML::SAX
It is also recommended that XML::SAX::ExpatXS be installed and made the default
XML::SAX parser using , along with the Expat library () for faster parsing.
XML::SAX::Expat is not recommended; XML::SAX::ExpatXS is considered the current
replacement for XML::SAX:Expat and is actively being considered to replace
XML::SAX::Expat. XML::SAX::Expat will work, but only if you have local copies of
the NCBI BLAST DTDs. This is due to issues with NCBI's BLAST XML format. The
DTDs and the web address to obtain them are:
NCBI_BlastOutput.dtd
NCBI_BlastOutput.mod.dtd
http://www.ncbi.nlm.nih.gov/data_specs/dtd/
=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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=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 the
web:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=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::SearchIO::blastxml;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::SearchIO);
use Bio::Root::Root;
use XML::SAX;
use IO::File;
use Bio::SearchIO::XML::BlastHandler;
use Bio::SearchIO::IteratedSearchResultEventBuilder;
our $DEBUG;
my %VALID_TYPE = (
'BLAST' => 'Bio::SearchIO::XML::BlastHandler',
'PSIBLAST' => 'Bio::SearchIO::XML::PsiBlastHandler',
'PSI-BLAST' => 'Bio::SearchIO::XML::PsiBlastHandler'
);
# mapping of NCBI Blast terms to Bioperl hash keys
=head2 new
Title : new
Usage : my $searchio = Bio::SearchIO->new(-format => 'blastxml',
-file => 'filename',
-tempfile => 1);
Function: Initializes the object - this is chained through new in SearchIO
Returns : Bio::SearchIO::blastxml object
Args : One additional argument from the format and file/fh parameters.
-tempfile => boolean. Defaults to false. Write out XML data
to a temporary filehandle to send to PerlSAX parser.
=cut
=head2 _initialize
Title : _initialize
Usage : private
Function: Initializes the object - this is chained through new in SearchIO
=cut
sub _initialize{
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($usetempfile, $blasttype,$xmlcompact) = $self->_rearrange([qw(
TEMPFILE
BLASTTYPE
XMLCOMPACT)],@args);
$blasttype ||= 'BLAST';
$self->{_xml_compact} = $xmlcompact || 0;
$self->blasttype(uc $blasttype);
defined $usetempfile && $self->use_tempfile($usetempfile);
$self->{_result_count} = 0;
eval { require Time::HiRes };
if( $@ ) { $DEBUG = 0; }
$DEBUG = 1 if( ! defined $DEBUG && ($self->verbose > 0));
}
=head2 next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result {
my ($self) = @_;
my $result;
my ($tfh);
# XMLCOMPACT
# WU-BLAST has an XML_COMPACT option which needs to be preprocessed before
# passing on to the parser.
if ($self->{_xml_compact}) {
$self->debug("XMLCOMPACT mode\n");
my ($tfh2, $filename) = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
$tfh2->autoflush(1);
my $fh = $self->_fh;
while (my $line = <$fh>) {
$line =~ s/></>\n</g;
print $tfh2 $line;
}
seek($tfh2,0,0);
close $fh;
# redirect self's IO to use new tempfile
$self->_fh($tfh2);
}
if( $self->use_tempfile ) {
$tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
$tfh->autoflush(1);
}
my $okaytoprocess = ($self->blasttype =~ /PSI/) ? $self->_chunk_psiblast($tfh) :
$self->_chunk_normalblast($tfh);
return unless( $okaytoprocess);
my %parser_args;
if( defined $tfh ) {
seek($tfh,0,0);
%parser_args = ('Source' => { 'ByteStream' => $tfh });
} else {
%parser_args = ('Source' => { 'String' => $self->{'_blastdata'} });
}
my $starttime;
if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; }
eval {
$result = $self->{'_xmlparser'}->parse(%parser_args);
};
if( $@ ) {
$self->warn("error in parsing a report:\n $@");
$result = undef;
}
if( $DEBUG ) {
$self->debug( sprintf("parsing took %f seconds\n", Time::HiRes::tv_interval($starttime)));
}
# parsing magic here - but we call event handlers rather than
# instantiating things
if (defined $result) {
# result count is handled here, as the BLASTXML reports are
# broken up into smaller easier to digest bits
$self->{_result_count}++;
return $result;
} else {
return;
}
}
=head2 result_count
Title : result_count
Usage : $num = $stream->result_count;
Function: Gets the number of Blast results that have been successfully parsed
at the point of the method call. This is not the total # of results
in the file.
Returns : integer
Args : none
Throws : none
=cut
sub result_count {
my $self = shift;
return $self->{_result_count};
}
=head2 use_tempfile
Title : use_tempfile
Usage : $obj->use_tempfile($newval)
Function: Get/Set boolean flag on whether or not use a tempfile
Example :
Returns : value of use_tempfile
Args : newvalue (optional)
=cut
sub use_tempfile{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_use_tempfile'} = $value;
}
return $self->{'_use_tempfile'};
}
=head2 blasttype
Title : blasttype
Usage : $obj->blasttype($newtype)
Function: Get/Set BLAST report type.
Returns : BLAST report type
Args : case-insensitive string of types BLAST or PSIBLAST (default: BLAST)
Note : this is used to determine how reports are 'chunked' (in cases
where multiple queries are submitted) and which XML handler
to use when parsing the report(s)
=cut
sub blasttype{
my ($self,$value) = @_;
if ($value) {
$self->throw("$value is not a supported BLAST type") unless exists $VALID_TYPE{$value};
my $ok;
eval {
$ok = $self->_load_module($VALID_TYPE{$value});
};
if ($@) {
print STDERR <<END;
$self: data module $VALID_TYPE{$value} cannot be found
Exception $@
For more information about the Bio::SearchIO::blastxml system please see the Bio::SearchIO::blastxml.
END
return unless $ok;
}
# BlastHandler does the heavy lifting
my $xmlhandler = $VALID_TYPE{$value}->new(-verbose => $self->verbose);
# The XML handler does the heavy work, passes data to object handler
if ($value =~ /^PSI/) {
my $handler = Bio::SearchIO::IteratedSearchResultEventBuilder->new();
$self->{'_handler'} = $handler; # cache
}
$xmlhandler->eventHandler($self->_eventHandler());
# start up the parser factory
my $parserfactory = XML::SAX::ParserFactory->parser(
Handler => $xmlhandler);
$self->{'_xmlparser'} = $parserfactory;
$self->saxparser(ref($parserfactory));
$self->{'_blasttype'} = $value;
}
return $self->{'_blasttype'};
}
sub saxparser {
my $self = shift;
return ref($self->{'_xmlparser'});
}
sub _chunk_normalblast {
my ($self, $tfh) = @_;
local $/ = "\n";
local $_;
$self->{'_blastdata'} = '';
my ($sawxmlheader, $okaytoprocess);
my $mode = 'header';
my $tail = << 'XML_END';
</BlastOutput_iterations>
</BlastOutput>
XML_END
# no buffering needed (famous last words...)
my $fh = $self->_fh;
#chop up XML into edible bits for the parser
while( defined( my $line = <$fh>) ) {
next if $line =~ m{^\s*</BlastOutput_iterations>}xmso || $line =~ m{^</BlastOutput>}xmso;
if( $line =~ m{^RPS-BLAST}i ) {
$self->{'_type'} = 'RPS-BLAST';
next;
} elsif ($line =~ m{^<\?xml\sversion="1.0"}xms) {# <?xml version="1.0"?> & <?xml version="1.0" encoding="UTF-8"?>
delete $self->{'_header'} if exists $self->{'_header'};
$sawxmlheader++;
$mode = 'header';
} elsif ($line =~ m{^\s*<Iteration>}xmso) {
if (!$sawxmlheader) {
if (defined $tfh) {
print $tfh $self->{'_header'}
} else {
$self->{'_blastdata'} .= $self->{'_header'};
}
}
$mode = 'iteration';
} elsif ($line =~ m{^\s*</Iteration>}xmso) {
if (defined $tfh) {
print $tfh $line.$tail;
} else {
$self->{'_blastdata'} .= $line.$tail;
}
$okaytoprocess++;
last;
}
if (defined $tfh) {
print $tfh $line;
} else {
$self->{'_blastdata'} .= $line;
}
$self->{"_$mode"} .= $line if $mode eq 'header';
}
return $okaytoprocess;
}
sub _chunk_psiblast {
my ($self, $tfh) = @_;
local $/ = "\n";
local $_;
$self->{'_blastdata'} = '';
my ($sawxmlheader, $okaytoprocess);
# no buffering needed (famous last words...)
my $fh = $self->_fh;
#chop up XML into edible bits for the parser
while( defined( my $line = <$fh>) ) {
if (defined $tfh) {
print $tfh $line;
} else {
$self->{'_blastdata'} .= $line;
}
#$self->{"_$mode"} .= $line;
if ($line =~ m{^</BlastOutput>}xmso) {
$okaytoprocess++;
last;
}
}
#$self->debug($self->{'_blastdata'}."\n");
return $okaytoprocess;
}
1;