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# $Id: wise.pm,v 1.6.4.1 2006/10/02 23:10:26 sendu Exp $
#
# BioPerl module for Bio::SearchIO::wise
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 48 lines of Pod
=head1 NAME
Bio::SearchIO::wise - Parsing of wise output as alignments
=head1 SYNOPSIS
  use Bio::SearchIO;
  my $parser = new Bio::SearchIO(-file    => 'file.genewise', 
                                 -format  => 'wise',
                                 -wisetype=> 'genewise');
  while( my $result = $parser->next_result ) {}
=head1 DESCRIPTION
This object parsers Wise output using Bio::Tools::Genewise or
Bio::Tools::Genomewise as a helper.
=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 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-dot-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::wise;
use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS);
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::SearchIO);
%MODEMAP = ('WiseOutput' => 'result',
            'Hit'             => 'hit',
            'Hsp'             => 'hsp'
    );
%MAPPING =
    (
     '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_qseq'      =>  'HSP-query_seq',
     'Hsp_hseq'      =>  'HSP-hit_seq',
     'Hsp_midline'   =>  'HSP-homology_seq',
     'Hsp_score'     =>  'HSP-score',
     'Hsp_qlength'   =>  'HSP-query_length',
     'Hsp_hlength'   =>  'HSP-hit_length',
     'Hsp_align-len' =>  'HSP-hsp_length',
     'Hsp_positive'   => 'HSP-conserved',
     'Hsp_identity'   => 'HSP-identical',
     #'Hsp_gaps'       => 'HSP-hsp_gaps',
     #'Hsp_hitgaps'    => 'HSP-hit_gaps',
     #'Hsp_querygaps'  => 'HSP-query_gaps',
      
     'Hit_id'        => 'HIT-name',
#    'Hit_desc'      => 'HIT-description',
#    'Hit_len'       => 'HIT-length',
     'Hit_score'     => 'HIT-score',
     'WiseOutput_program'   => 'RESULT-algorithm_name',
     'WiseOutput_query-def' => 'RESULT-query_name',
     'WiseOutput_query-desc'=> 'RESULT-query_description',
     'WiseOutput_query-len' => 'RESULT-query_length',
    );
$DEFAULT_WRITER_CLASS = 'Bio::Search::Writer::HitTableWriter';
use Bio::Tools::Genewise;
use Bio::Tools::Genomewise;
HideShow 11 lines of Pod
=head2 new
 Title   : new
 Usage   : my $obj = new Bio::SearchIO::wise();
 Function: Builds a new Bio::SearchIO::wise object 
 Returns : an instance of Bio::SearchIO::wise
 Args    : -wise => a Bio::Tools::Genewise or Bio::Tools::Genomewise object
=cut
sub _initialize {
    my ($self,@args) = @_;
    my ( $wisetype, $file,$fh ) =
        $self->_rearrange([qw(WISETYPE FILE FH)], @args);
    my @newargs;
    while( @args ) {
        my $a = shift @args;
        if( $a =~ /FILE|FH/i ) {
            shift @args;
            next;
        }
        push @newargs, $a, shift @args;
    }
    $self->SUPER::_initialize(@newargs);
    # Optimization: caching the EventHandler 
    # since it's use a lot during the parse.
    $self->{'_handler_cache'} = $self->_eventHandler;
    $self->wisetype($wisetype);
    my @ioargs;
    if( $fh ) { 
        push @ioargs, ('-fh' => $fh);
    } elsif( $file ) {
        push @ioargs, ('-file' => $file);
    }
    if( $wisetype =~ /genewise/i ) {
        $self->wise(new Bio::Tools::Genewise(@ioargs));
    } elsif( $wisetype =~ /genomewise/i ) {
        $self->wise(new Bio::Tools::Genomewise(@ioargs));
    } else { 
        $self->throw("Must supply a -wisetype to ".ref($self)." which is one of 'genomewise' 'genewise'\n");
    }
    return $self;
}
HideShow 10 lines of Pod
=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) = @_;
   local $/ = "\n";
   local $_;
   return unless $self->wise;
   my $prediction = $self->wise->next_prediction;
   return unless $prediction;
   $self->{'_reporttype'} = uc $self->wisetype;
   $self->start_element({'Name' => 'WiseOutput'});
   $self->element({'Name' => 'WiseOutput_program',
                   'Data' => $self->wisetype});
   $self->element({'Name' => 'WiseOutput_query-def',
                   'Data' => $self->wise->_target_id});
   my @transcripts = $prediction->transcripts;
   foreach my $transcript ( @transcripts ) {
       my @exons =  $transcript->exons;
       my $protid;
       $self->start_element({'Name' => 'Hit'});
        
       if( $exons[0]->has_tag('supporting_feature') ) {
           my ($supporting_feature) = $exons[0]->get_tag_values('supporting_feature');
           $protid = $supporting_feature->feature2->seq_id;
           $self->element({'Name' => 'Hit_id',
                           'Data' => $protid});       
       } 
       $self->element({'Name' => 'Hit_score',
                       'Data' => $exons[0]->score});
       foreach my $exon ( @exons ) {
           $self->start_element({'Name' => 'Hsp'});
           if( $exon->strand < 0 ) { 
               $self->element({'Name' => 'Hsp_query-from',
                               'Data' => $exon->end});
               $self->element({'Name' => 'Hsp_query-to',
                               'Data' => $exon->start});
           } else { 
               $self->element({'Name' => 'Hsp_query-from',
                               'Data' => $exon->start});
               $self->element({'Name' => 'Hsp_query-to',
                               'Data' => $exon->end});
           }
           $self->element({'Name' => 'Hsp_score',
                           'Data' => $exon->score});
           if( $exon->has_tag('supporting_feature') ) {
               my ($sf) = $exon->get_tag_values('supporting_feature');
               my $protein = $sf->feature2;
               if( $protein->strand < 0 ) {
                   $self->element({'Name' => 'Hsp_hit-from',
                                   'Data' => $protein->end});
                   $self->element({'Name' => 'Hsp_hit-to',
                                   'Data' => $protein->start});
               } else { 
                   $self->element({'Name' => 'Hsp_hit-from',
                                   'Data' => $protein->start});
                   $self->element({'Name' => 'Hsp_hit-to',
                                   'Data' => $protein->end});
               }
           }
           $self->element({'Name' => 'Hsp_identity',
                           'Data' => 0});
           $self->element({'Name' => 'Hsp_positive',
                           'Data' => 0});
           $self->end_element({'Name' => 'Hsp'});
       }
       $self->end_element({'Name' => 'Hit'});
   }
   $self->end_element({'Name' => 'WiseOutput'});
   return $self->end_document();
}
HideShow 11 lines of Pod
=head2 start_element
 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub start_element{
   my ($self,$data) = @_;
   # we currently don't care about attributes
   my $nm = $data->{'Name'};
   my $type = $MODEMAP{$nm};
   if( $type ) {
       if( $self->_eventHandler->will_handle($type) ) {
           my $func = sprintf("start_%s",lc $type);
           $self->_eventHandler->$func($data->{'Attributes'});
       }
       unshift @{$self->{'_elements'}}, $type;
       if($type eq 'result') {
           $self->{'_values'} = {};
           $self->{'_result'}= undef;
       }
   }
}
HideShow 11 lines of Pod
=head2 end_element
 Title   : start_element
 Usage   : $eventgenerator->end_element
 Function: Handles an end element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    my $rc;
    if( $type = $MODEMAP{$nm} ) {
        if( $self->_eventHandler->will_handle($type) ) {
            my $func = sprintf("end_%s",lc $type);
            $rc = $self->_eventHandler->$func($self->{'_reporttype'},
                                              $self->{'_values'});
        }
        shift @{$self->{'_elements'}};
    } 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'};
        }
    } else {
        $self->debug( "unknown nm $nm, ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at
                                # end of an element
    $self->{'_result'} = $rc if( defined $type && $type eq 'result' );
    return $rc;
}
HideShow 11 lines of Pod
=head2 element
 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'
=cut
sub element{
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}
HideShow 11 lines of Pod
=head2 characters
 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string
=cut
sub characters{
   my ($self,$data) = @_;
   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
   $self->{'_last_data'} = $data->{'Data'};
}
HideShow 13 lines of Pod
=head2 within_element
 Title   : within_element
 Usage   : if( $eventgenerator->within_element($element) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name
=cut
sub within_element{
   my ($self,$name) = @_;
   return 0 if ( ! defined $name &&
                 ! defined  $self->{'_elements'} ||
                 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
           return 1;
       }
   }
   return 0;
}
HideShow 13 lines of Pod
=head2 in_element
 Title   : in_element
 Usage   : if( $eventgenerator->in_element($element) ) {}
 Function: Test if we are in a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name
=cut
sub in_element{
   my ($self,$name) = @_;
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}
HideShow 11 lines of Pod
=head2 start_document
 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none
=cut
sub start_document{
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_elements'} = [];
    $self->{'_reporttype'} = 'exonerate';
}
HideShow 11 lines of Pod
=head2 end_document
 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none
=cut
sub end_document{
   my ($self,@args) = @_;
   return $self->{'_result'};
}
sub write_result {
   my ($self, $blast, @args) = @_;
   if( not defined($self->writer) ) {
       $self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS");
       $self->writer( $DEFAULT_WRITER_CLASS->new() );
   }
   $self->SUPER::write_result( $blast, @args );
}
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
sub report_count { shift->result_count }
HideShow 11 lines of Pod
=head2 wise
 Title   : wise
 Usage   : $obj->wise($newval)
 Function: Get/Set the Wise object parser
 Returns : value of wise (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub wise{
    my $self = shift;
    return $self->{'wise'} = shift if @_;
    return $self->{'wise'};
}
HideShow 11 lines of Pod
=head2 wisetype
 Title   : wisetype
 Usage   : $obj->wisetype($newval)
 Function: Wise program type
 Returns : value of wisetype (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub wisetype{
    my $self = shift;
    return $self->{'wisetype'} = shift if @_;
    return $self->{'wisetype'};
}
1;