Bio::SearchIO psl
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SearchIO::psl - A parser for PSL output (UCSC)
Package variables
No package variables defined.
Included modules
Bio::Search::HSP::HSPFactory
Bio::Search::Hit::HitFactory
Bio::Search::Result::ResultFactory
Bio::SearchIO
Inherit
Bio::SearchIO
Synopsis
  use Bio::SearchIO;
  my $parser = new Bio::SearchIO(-file   => 'file.psl',
                                 -format => 'psl');
  while( my $result = $parser->next_result ) {
  }
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 => 'BLASTZ' when initializing the
SearchIO object.
Methods
_initialize
No description
Code
next_resultDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
_modeDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
result_countDescriptionCode
report_count
No description
Code
program_nameDescriptionCode
Methods description
next_resultcode    nextTop
 Title   : next_result
 Usage   : my $result = $parser->next_result
 Function: Parse the next result from the data stream
 Returns : Bio::Search::Result::ResultI
 Args    : none
start_elementcodeprevnextTop
 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_elementcodeprevnextTop
 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'
elementcodeprevnextTop
 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'
characterscodeprevnextTop
 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string
_modecodeprevnextTop
 Title   : _mode
 Usage   : $obj->_mode($newval)
 Function: 
 Example : 
 Returns : value of _mode
 Args    : newvalue (optional)
within_elementcodeprevnextTop
 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_elementcodeprevnextTop
 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_documentcodeprevnextTop
 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handles a start document event
 Returns : none
 Args    : none
end_documentcodeprevnextTop
 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none
result_countcodeprevnextTop
 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none
program_namecodeprevnextTop
 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)
Methods code
_initializedescriptionprevnextTop
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'));
    $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::PSLHSP'));
}
next_resultdescriptionprevnextTop
sub next_result {
   my ($self) = @_;
   my ($lastquery,$lasthit) = undef;
   local $_ = "\n";

   #clear header if exists
   my $head = $self->_readline;
   if($head =~ /^psLayout/){
       for(1..4){$self->_readline}
   } else {
     $self->_pushback($head);
   }

   while( defined ($_ = $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 $self->end_document;
   }
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($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;
	$self->{'_mode'} = '';
    }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($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 $rc;
}
elementdescriptionprevnextTop
sub element {
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}
charactersdescriptionprevnextTop
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'} = $data->{'Data'};
}
_modedescriptionprevnextTop
sub _mode {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_mode'} = $value;
    }
    return $self->{'_mode'};
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($self,$name) = @_;  
   return 0 if ( ! defined $name &&
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
	   return 1;
       } 
   }
   return 0;
}
in_elementdescriptionprevnextTop
sub in_element {
   my ($self,$name) = @_;  
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_mode'} = '';
    $self->{'_elements'} = [];
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
report_countdescriptionprevnextTop
sub report_count {
 shift->result_count
}
program_namedescriptionprevnextTop
sub program_name {
    my $self = shift;

    $self->{'program_name'} = shift if @_;
    return $self->{'program_name'} || $DefaultProgramName;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/MailList.shtml  - About the mailing lists
Reporting BugsTop
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.bioperl.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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    :