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# $Id: psl.pm,v 1.13.4.1 2006/10/02 23:10:26 sendu Exp $
#
# BioPerl module for Bio::SearchIO::psl
#
# 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 52 lines of Pod
=head1 NAME
Bio::SearchIO::psl - A parser for PSL output (UCSC)
=head1 SYNOPSIS
  use Bio::SearchIO;
  my $parser = new Bio::SearchIO(-file   => 'file.psl',
                                 -format => 'psl');
  while( my $result = $parser->next_result ) {
  }
=head1 DESCRIPTION
This is a SearchIO driver for PSL format.
PSL format is documented here:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL
By default it assumes PSL output came from BLAT you can override that
by specifying -program_name =E<gt> 'BLASTZ' when initializing the
SearchIO object.
=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::psl;
use vars qw(%MAPPING %MODEMAP $DEFAULT_WRITER_CLASS $DefaultProgramName);
use strict;
use Bio::Search::HSP::HSPFactory;
use Bio::Search::Hit::HitFactory;
use Bio::Search::Result::ResultFactory;
$DefaultProgramName = 'BLAT';
$DEFAULT_WRITER_CLASS = 'Bio::Search::Writer::HitTableWriter';
# mapping of terms to Bioperl hash keys
%MODEMAP = (
            'PSLOutput'          => 'result',
            'Result'             => 'result',
            'Hit'                => 'hit',
            'Hsp'                => 'hsp'
            );
%MAPPING = ( 
             '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_mismatches' => 'HSP-mismatches',
             'Hsp_qgapblocks' => 'HSP-query_gapblocks',
             'Hsp_hgapblocks' => 'HSP-hit_gapblocks',
             'Hsp_gaps'       => 'HSP-hsp_gaps',
             'Hsp_hitgaps'    => 'HSP-hit_gaps',
             'Hsp_querygaps'  => 'HSP-query_gaps',
             'Hsp_align-len'  => 'HSP-hsp_length',
             'Hsp_query-frame'=> 'HSP-query_frame',
             'Hsp_hit-frame'  => 'HSP-hit_frame',
             'Hit_id'        => 'HIT-name',
             'Hit_len'       => 'HIT-length',
             'Hit_accession' => 'HIT-accession',
             'Hit_def'       => 'HIT-description',
             'Hit_signif'    => 'HIT-significance',
             'Hit_score'     => 'HIT-score',
             'Hit_bits'      => 'HIT-bits',
             'PSLOutput_program'  => 'RESULT-algorithm_name',
             'PSLOutput_version'  => 'RESULT-algorithm_version',
             'PSLOutput_query-def'=> 'RESULT-query_name',
             'PSLOutput_query-len'=> 'RESULT-query_length',
             'PSLOutput_query-acc'=> 'RESULT-query_accession',
             'PSLOutput_querydesc'=> 'RESULT-query_description',
             'PSLOutput_db'       => 'RESULT-database_name',
             'PSLOutput_db-len'   => 'RESULT-database_entries',
             'PSLOutput_db-let'   => 'RESULT-database_letters',
             );
use base qw(Bio::SearchIO);
HideShow 11 lines of Pod
=head2 new
 Title   : new
 Usage   : my $obj = new Bio::SearchIO::psl();
 Function: Builds a new Bio::SearchIO::psl object 
 Returns : an instance of Bio::SearchIO::psl
 Args    :
=cut
sub _initialize {
    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    my ($pname) = $self->_rearrange([qw(PROGRAM_NAME)],
                                    @args);
    $self->program_name($pname || $DefaultProgramName);
    $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult'));
    $self->_eventHandler->register_factory('hit', Bio::Search::Hit::HitFactory->new(-type => 'Bio::Search::Hit::GenericHit'));
    $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::PSLHSP'));
}
HideShow 11 lines of Pod
=head2 next_result
 Title   : next_result
 Usage   : my $result = $parser->next_result
 Function: Parse the next result from the data stream
 Returns : L<Bio::Search::Result::ResultI>
 Args    : none
=cut
sub next_result{
   my ($self) = @_;
   my ($lastquery,$lasthit);
   local $/ = "\n";
   local $_;
   while( defined ($_ = $self->_readline) ) {
            #clear header if exists
            if(/^psLayout/){
                        #pass over header lines lines
                        while(!/^\d+\s+\d+\s+/) {
                                $_ = $self->_readline;
                        }
            } 
                my ( $matches,$mismatches,$rep_matches,$n_count,
            $q_num_insert,$q_base_insert,
            $t_num_insert, $t_base_insert, 
            $strand, $q_name, $q_length, $q_start,
            $q_end, $t_name, $t_length,$t_start, $t_end, $block_count,
            $block_sizes,  $q_starts,      $t_starts
            ) = split;
       my $score   = sprintf "%.2f", ( 100 * ( $matches + $mismatches + $rep_matches ) / $q_length );
       # this is overall percent identity...
       my $percent_id = sprintf "%.2f", ( 100 * ($matches + $rep_matches)/( $matches + $mismatches + $rep_matches )
);
       # Remember Jim's code is 0 based
       if( defined $lastquery && 
           $lastquery ne $q_name ) {
           $self->end_element({'Name' => 'Hit'});
           $self->end_element({'Name' => 'PSLOutput'});
           $self->_pushback($_);
           return $self->end_document;
       } elsif( ! defined $lastquery ) {
           $self->{'_result_count'}++;
           $self->start_element({'Name' => 'PSLOutput'});
           $self->element({'Name' => 'PSLOutput_program',
                           'Data' => $self->program_name});
           $self->element({'Name' => 'PSLOutput_query-def',
                           'Data' => $q_name});
           $self->element({'Name' => 'PSLOutput_query-len',
                           'Data' => $q_length});
           $self->start_element({'Name' => 'Hit'});
           $self->element({'Name' => 'Hit_id',
                           'Data' => $t_name});
           $self->element({'Name' => 'Hit_len',
                           'Data' => $t_length});
           $self->element({'Name' => 'Hit_score',
                           'Data' => $score});
       } elsif( $lasthit ne $t_name ) {
           $self->end_element({'Name' => 'Hit'});
           $self->start_element({'Name' => 'Hit'});
           $self->element({'Name' => 'Hit_id',
                           'Data' => $t_name});
           $self->element({'Name' => 'Hit_len',
                           'Data' => $t_length});
           $self->element({'Name' => 'Hit_score',
                           'Data' => $score});
       }
               
       my $identical = $matches + $rep_matches;
       $self->start_element({'Name' => 'Hsp'});
       $self->element({'Name' => 'Hsp_score',
                       'Data' => $score});
       $self->element({'Name' => 'Hsp_identity',
                       'Data' => $identical});
       $self->element({'Name' => 'Hsp_positive',
                       'Data' => $identical});
       $self->element({'Name' => 'Hsp_mismatches',
                       'Data' => $mismatches});
       $self->element({'Name' => 'Hsp_gaps',
                       'Data' => $q_base_insert + $t_base_insert});
       # query gaps are the number of target inserts and vice-versa
       $self->element({'Name' => 'Hsp_querygaps',
                       'Data' => $t_base_insert});
       $self->element({'Name' => 'Hsp_hitgaps',
                       'Data' => $q_base_insert});
       if( $strand eq '+' ) {
           $self->element({'Name' => 'Hsp_query-from',
                           'Data' => $q_start + 1});
           $self->element({'Name' => 'Hsp_query-to',
                           'Data' => $q_end});
       } else { 
           $self->element({'Name' => 'Hsp_query-to',
                           'Data' => $q_start + 1});
           $self->element({'Name' => 'Hsp_query-from',
                           'Data' => $q_end});
       }
       my $hsplen = $q_base_insert + $t_base_insert + 
           abs( $t_end - $t_start) + abs( $q_end - $q_start);
       $self->element({'Name' => 'Hsp_hit-from',
                       'Data' => $t_start + 1 });
       $self->element({'Name' => 'Hsp_hit-to',
                       'Data' => $t_end});
       $self->element({'Name' => 'Hsp_align-len',
                       'Data' => $hsplen});
       # cleanup trailing commas in some output
       $block_sizes =~ s/\,$//;
       $q_starts    =~ s/\,$//;
       $t_starts    =~ s/\,$//;
       my @blocksizes = split(/,/,$block_sizes); # block sizes
       my @qstarts = split(/,/,$q_starts); # starting position of each block
                                           # in query
       my @tstarts = split(/,/,$t_starts); # starting position of each block
                                           # in target
       my (@qgapblocks,@hgapblocks);
       for( my $i = 0; $i < $block_count; $i++) {
           if( $strand eq '+' ) {
               push @qgapblocks, [ $qstarts[$i] + 1, $blocksizes[$i]];
           } else { 
               push @qgapblocks, [ $q_length - $qstarts[$i], $blocksizes[$i]];
           }
           push @hgapblocks, [ $tstarts[$i] + 1, $blocksizes[$i]];
       }
       $self->element({'Name' => 'Hsp_qgapblocks',
                       'Data' => \@qgapblocks});
       $self->element({'Name' => 'Hsp_hgapblocks',
                       'Data' => \@hgapblocks});
       $self->end_element({'Name' => 'Hsp'});
       $lastquery = $q_name;
       $lasthit   = $t_name;
   }   
   if( defined $lasthit || defined $lastquery ) {
       $self->end_element({'Name' => 'Hit'});
       $self->end_element({'Name' => 'Result'});
       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'};    
   if( my $type = $MODEMAP{$nm} ) {
        $self->_mode($type);
        if( $self->_eventHandler->will_handle($type) ) {
            my $func = sprintf("start_%s",lc $type);
            $self->_eventHandler->$func($data->{'Attributes'});
        }                                                
        unshift @{$self->{'_elements'}}, $type;
    }
    if($nm eq 'PSLOutput') {
        $self->{'_values'} = {};
        $self->{'_result'}= undef;
        $self->{'_mode'} = '';
    }
}
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 $rc;
    # Hsp are sort of weird, in that they end when another
    # object begins so have to detect this in end_element for now
         
    if( my $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 { 
        $self->warn( __PACKAGE__."::end_element: unknown nm '$nm', ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
                                # end of an element
    $self->{'_result'} = $rc if( defined $nm &&
                                 defined $MODEMAP{$nm} &&
                                 $MODEMAP{$nm} 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'} );
   if( $data->{'Data'} =~ /^\s+$/ ) {
       return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
   }
   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
        
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  
    
   $self->{'_last_data'} = $data->{'Data'}; 
}
HideShow 12 lines of Pod
=head2 _mode
 Title   : _mode
 Usage   : $obj->_mode($newval)
 Function: 
 Example : 
 Returns : value of _mode
 Args    : newvalue (optional)
=cut
sub _mode{
    my ($self,$value) = @_;
    if( defined $value) {
        $self->{'_mode'} = $value;
    }
    return $self->{'_mode'};
}
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   : $eventgenerator->start_document
 Function: Handles a start document event
 Returns : none
 Args    : none
=cut
sub start_document{
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_mode'} = '';
    $self->{'_elements'} = [];
}
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'};
}
HideShow 11 lines of Pod
=head2 result_count
 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none
=cut
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
sub report_count { shift->result_count }
HideShow 11 lines of Pod
=head2 program_name
 Title   : program_name
 Usage   : $obj->program_name($newval)
 Function: Get/Set the program name
 Returns : value of program_name (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
=cut
sub program_name{
    my $self = shift;
    $self->{'program_name'} = shift if @_;
    return $self->{'program_name'} || $DefaultProgramName;
}
1;