Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.

SYNOPSIS

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  # This is not to be used directly.

DESCRIPTION

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This is the XML handler for BLAST PSIBLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for Bio::Search object generation.

This was recently split off from the original code for Bio::SearchIO::blastxml primarily for maintenance purposes.

DEPENDENCIES

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In addition to parts of the Bio:: hierarchy, this module uses:

 XML::SAX::Base

which comes with the XML::SAX distribution.

FEEDBACK

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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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich, Chris Fields

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Email jason-at-bioperl.org Email cjfields-at-uiuc dot edu

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

SAX methods

start_document

 Title   : start_document
 Usage   : $parser->start_document;
 Function: SAX method to indicate starting to parse a new document
 Returns : none
 Args    : none

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

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

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

characters

 Title   : characters
 Usage   : $parser->characters($data)
 Function: Signals new characters to be processed
 Returns : characters read
 Args    : hash ref with the key 'Data'
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::SearchIO::XML::PsiBlastHandler
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich, Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


# Let the code begin...
package Bio::SearchIO::XML::PsiBlastHandler;
use base qw(Bio::Root::Root XML::SAX::Base);

my %MODEMAP = (
    'BlastOutput'   => 'result',
    'Iteration'     => 'iteration',
    'Hit'           => 'hit',
    'Hsp'           => 'hsp'
);

# MAPPING is distinct from BlastHandler, can't really mix the two...

my %MAPPING = (
                # Result-specific fields
                'BlastOutput_program'   => 'RESULT-algorithm_name',
                'BlastOutput_version'   => 'RESULT-algorithm_version',
                'BlastOutput_db'        => 'RESULT-database_name',
                'BlastOutput_reference' => 'RESULT-program_reference',
                'BlastOutput_query-def' => 'RESULT-query_description',
                'BlastOutput_query-len' => 'RESULT-query_length',
                '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'},

                # Iteration-specific parameters
                'Iteration_iter-num'  => 'ITERATION-number',
                'Iteration_converged' => 'ITERATION-converged',

                # 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',

                # 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',
               );

# these XML tags are ignored for now
my %IGNOREDTAGS = (
                'Hsp_num'              => 1,#'HSP-order',
                'Hsp_pattern-from'     => 1,#'patternend',
                'Hsp_pattern-to'       => 1,#'patternstart',
                'Hsp_density'          => 1,#'hspdensity',
                'Iteration_message'    => 1,
                'Hit_hsps'             => 1,
                'BlastOutput_param'    => 1,
                'Iteration_hits'       => 1,
                'Statistics'           => 1,
                'Parameters'           => 1,
                'BlastOutput'          => 1,
                'BlastOutput_iterations' => 1,
                   );


sub start_document{
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= [];
}


sub end_document{
   my ($self,@args) = @_;
   
   # reset data carried throughout parse
   $self->{'_resultdata'} = undef;
   
   # pass back ref to results queue; caller must reset handler results queue
   return $self->{'_result'};
}


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'});
        }                                                    
    }
}


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 $1; 
    }
    if ($nm eq 'Iteration') {
        map {
            $self->{'_values'}->{$_} = $self->{'_resultdata'}->{$_};
            } keys %{ $self->{'_resultdata'} };
    }
    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( exists $MAPPING{$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( exists $IGNOREDTAGS{$nm} ){
        # ignores these elements for now
    }
    else {      
        $self->debug("ignoring unrecognized element type $nm\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
                                # end of an element
                                
    # add to ResultI array
    $self->{'_result'} = $rc if( $nm eq 'BlastOutput' );
    # reset values for each Result round
    if ($nm eq 'BlastOutput') {
        $self->{'_values'} = {};
    }
}


sub characters{
   my ($self,$data) = @_;
   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
   $self->{'_last_data'} .= $data->{'Data'};
}

sub eventHandler {
    my $self = shift;
    return $self->{'_handler'} = shift if @_;
    return $self->{'_handler'};
}

1;