view variant_effect_predictor/Bio/SearchIO/blastxml.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

# $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 <[e-mail]>
#
# 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.

  [e-mail]              - 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:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Jason Stajich

Email [e-mail]

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/\&apos;/\`/g;	
#	s/\&gt;/\>/g;
#	s/\&lt;/\</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;