Bio::SearchIO::wise - Parsing of wise output as alignments

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::SearchIO::wise - Parsing of wise output as alignments

SYNOPSIS

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  use Bio::SearchIO;
  my $parser = Bio::SearchIO->new(-file    => 'file.genewise', 
                                 -format  => 'wise',
                                 -wisetype=> 'genewise');

  while( my $result = $parser->next_result ) {}

DESCRIPTION

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This object parsers Wise output using Bio::Tools::Genewise or Bio::Tools::Genomewise as a helper.

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

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Email jason-at-bioperl-dot-org

APPENDIX

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

new

 Title   : new
 Usage   : my $obj = Bio::SearchIO::wise->new();
 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

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

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'

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'

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'

characters

 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string

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

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

start_document

 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none

end_document

 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none

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)

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)
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::SearchIO::wise
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# 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



# 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::SearchIO::Writer::HitTableWriter';


use Bio::Tools::Genewise;
use Bio::Tools::Genomewise;


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(Bio::Tools::Genewise->new(@ioargs));
    } elsif( $wisetype =~ /genomewise/i ) {
	$self->wise(Bio::Tools::Genomewise->new(@ioargs));
    } else { 
	$self->throw("Must supply a -wisetype to ".ref($self)." which is one of 'genomewise' 'genewise'\n");
    }
    return $self;
}



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->_prot_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' => $self->wise->_target_id});       
       } 
       $self->element({'Name' => 'Hit_score',
		       'Data' => $self->wise->_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' => $self->wise->_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();
}


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;
       }
   }

}


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;
}


sub element{
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}


sub characters{
   my ($self,$data) = @_;

   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );

   $self->{'_last_data'} = $data->{'Data'};
}


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;
}



sub in_element{
   my ($self,$name) = @_;
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}


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



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 }



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


sub wisetype{
    my $self = shift;

    return $self->{'wisetype'} = shift if @_;
    return $self->{'wisetype'};
}

1;