Raw content of Bio::SearchIO::blastxml
<![CDATA[# $Id: blastxml.pm,v 1.24 2002/10/26 09:32:16 sac Exp $
#
# BioPerl module for Bio::SearchIO::blastxml
#
# 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 = new Bio::SearchIO(-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 = new Bio::SearchIO(-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.
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 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@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails 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::SearchIO::blastxml;
use vars qw(@ISA $DTD %MAPPING %MODEMAP $DEBUG);
use strict;
$DTD = 'ftp://ftp.ncbi.nlm.nih.gov/blast/documents/NCBI_BlastOutput.dtd';
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::SearchIO;
use XML::Parser::PerlSAX;
use XML::Handler::Subs;
use HTML::Entities;
use IO::File;
BEGIN {
# mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = ('BlastOutput' => 'result',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
%MAPPING = (
# HSP specific fields
'Hsp_bit-score' => 'HSP-bits',
'Hsp_score' => 'HSP-score',
'Hsp_evalue' => 'HSP-evalue',
'Hsp_query-from' => 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
'Hsp_positive' => 'HSP-conserved',
'Hsp_identity' => 'HSP-identical',
'Hsp_gaps' => 'HSP-gaps',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_midline' => 'HSP-homology_seq',
'Hsp_align-len' => 'HSP-hsp_length',
'Hsp_query-frame'=> 'HSP-query_frame',
'Hsp_hit-frame' => 'HSP-hit_frame',
# these are ignored for now
'Hsp_num' => 'HSP-order',
'Hsp_pattern-from' => 'patternend',
'Hsp_pattern-to' => 'patternstart',
'Hsp_density' => 'hspdensity',
# Hit specific fields
'Hit_id' => 'HIT-name',
'Hit_len' => 'HIT-length',
'Hit_accession' => 'HIT-accession',
'Hit_def' => 'HIT-description',
'Hit_num' => 'HIT-order',
'Iteration_iter-num' => 'HIT-iteration',
'Iteration_stat' => 'HIT-iteration_statistic',
'BlastOutput_program' => 'RESULT-algorithm_name',
'BlastOutput_version' => 'RESULT-algorithm_version',
'BlastOutput_query-def' => 'RESULT-query_description',
'BlastOutput_query-len' => 'RESULT-query_length',
'BlastOutput_db' => 'RESULT-database_name',
'BlastOutput_reference' => 'RESULT-program_reference',
'BlastOutput_query-ID' => 'runid',
'Parameters_matrix' => { 'RESULT-parameters' => 'matrix'},
'Parameters_expect' => { 'RESULT-parameters' => 'expect'},
'Parameters_include' => { 'RESULT-parameters' => 'include'},
'Parameters_sc-match' => { 'RESULT-parameters' => 'match'},
'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch'},
'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen'},
'Parameters_gap-extend'=> { 'RESULT-parameters' => 'gapext'},
'Parameters_filter' => {'RESULT-parameters' => 'filter'},
'Statistics_db-num' => 'RESULT-database_entries',
'Statistics_db-len' => 'RESULT-database_letters',
'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength'},
'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace'},
'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' },
'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' },
'Statistics_entropy' => { 'RESULT-statistics' => 'entropy'},
);
eval { require Time::HiRes };
if( $@ ) { $DEBUG = 0; }
}
@ISA = qw(Bio::SearchIO );
=head2 new
Title : new
Usage : my $searchio = new Bio::SearchIO(-format => 'blastxml',
-file => 'filename',
-tempfile => 1);
Function: Initializes the object - this is chained through new in SearchIO
Returns : Bio::SearchIO::blastxml object
Args : One additional argument from the format and file/fh parameters.
-tempfile => boolean. Defaults to false. Write out XML data
to a temporary filehandle to send to
PerlSAX parser.
=cut
=head2 _initialize
Title : _initialize
Usage : private
Function: Initializes the object - this is chained through new in SearchIO
=cut
sub _initialize{
my ($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($usetempfile) = $self->_rearrange([qw(TEMPFILE)],@args);
defined $usetempfile && $self->use_tempfile($usetempfile);
$self->{'_xmlparser'} = new XML::Parser::PerlSAX();
$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 $data = '';
my $firstline = 1;
my ($tfh);
if( $self->use_tempfile ) {
$tfh = IO::File->new_tmpfile or $self->throw("Unable to open temp file: $!");
$tfh->autoflush(1);
}
my $okaytoprocess;
while( defined( $_ = $self->_readline) ) {
if( /^RPS-BLAST/i ) {
$self->{'_type'} = 'RPSBLAST';
next;
}
if( /^<\?xml version/ && ! $firstline) {
$self->_pushback($_);
last;
}
$_ = decode_entities($_);
# s/\'/\`/g;
# s/\>/\>/g;
# s/\</\</g;
$okaytoprocess = 1;
if( defined $tfh ) {
print $tfh $_;
} else {
$data .= $_;
}
$firstline = 0;
}
return undef unless( $okaytoprocess);
my %parser_args;
if( defined $tfh ) {
seek($tfh,0,0);
%parser_args = ('Source' => { 'ByteStream' => $tfh },
'Handler' => $self);
} else {
%parser_args = ('Source' => { 'String' => $data },
'Handler' => $self);
}
my $result;
my $starttime;
if( $DEBUG ) { $starttime = [ Time::HiRes::gettimeofday() ]; }
eval {
$result = $self->{'_xmlparser'}->parse(%parser_args);
$self->{'_result_count'}++;
};
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
return $result;
}
=head2 SAX methods
=cut
=head2 start_document
Title : start_document
Usage : $parser->start_document;
Function: SAX method to indicate starting to parse a new document
Returns : none
Args : none
=cut
sub start_document{
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'}= undef;
}
=head2 end_document
Title : end_document
Usage : $parser->end_document;
Function: SAX method to indicate finishing parsing a new document
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub end_document{
my ($self,@args) = @_;
return $self->{'_result'};
}
=head2 start_element
Title : start_element
Usage : $parser->start_element($data)
Function: SAX method to indicate starting a new element
Returns : none
Args : hash ref for data
=cut
sub start_element{
my ($self,$data) = @_;
# we currently don't care about attributes
my $nm = $data->{'Name'};
if( my $type = $MODEMAP{$nm} ) {
if( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf("start_%s",lc $type);
$self->_eventHandler->$func($data->{'Attributes'});
}
}
if($nm eq 'BlastOutput') {
$self->{'_values'} = {};
$self->{'_result'}= undef;
}
}
=head2 end_element
Title : end_element
Usage : $parser->end_element($data)
Function: Signals finishing an element
Returns : Bio::Search object dpending on what type of element
Args : hash ref for data
=cut
sub end_element{
my ($self,$data) = @_;
my $nm = $data->{'Name'};
my $rc;
if($nm eq 'BlastOutput_program' &&
$self->{'_last_data'} =~ /(t?blast[npx])/i ) {
$self->{'_type'} = uc $1;
}
if( my $type = $MODEMAP{$nm} ) {
if( $self->_eventHandler->will_handle($type) ) {
my $func = sprintf("end_%s",lc $type);
$rc = $self->_eventHandler->$func($self->{'_type'},
$self->{'_values'});
}
} elsif( $MAPPING{$nm} ) {
if ( ref($MAPPING{$nm}) =~ /hash/i ) {
my $key = (keys %{$MAPPING{$nm}})[0];
$self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
} else {
$self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
}
} elsif( $nm eq 'Iteration' || $nm eq 'Hit_hsps' || $nm eq 'Parameters' ||
$nm eq 'BlastOutput_param' || $nm eq 'Iteration_hits' ||
$nm eq 'Statistics' || $nm eq 'BlastOutput_iterations' ){
} else {
$self->debug("ignoring unrecognized element type $nm\n");
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if( $nm eq 'BlastOutput' );
return $rc;
}
=head2 characters
Title : characters
Usage : $parser->characters($data)
Function: Signals new characters to be processed
Returns : characters read
Args : hash ref with the key 'Data'
=cut
sub characters{
my ($self,$data) = @_;
return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
$self->{'_last_data'} = $data->{'Data'};
}
=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'};
}
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
1;
]]>