Bio::SearchIO sim4
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SearchIO::sim4 - parser for Sim4 alignments
Package variables
No package variables defined.
Included modules
Bio::SearchIO::SearchResultEventBuilder
POSIX
Inherit
Bio::SearchIO
Synopsis
  # do not use this module directly, it is a driver for SearchIO
  use Bio::SearchIO;
  my $searchio = new Bio::SearchIO(-file => 'results.sim4',
                                   -format => 'sim4');

  while ( my $result = $searchio->next_result ) {
      while ( my $hit = $result->next_hit ) {
	  while ( my $hsp = $hit->next_hsp ) {
              # ...
	  }
      }
  }
Description
This is a driver for the SearchIO system for parsing Sim4.
http://globin.cse.psu.edu/html/docs/sim4.html
Cannot parse LAV or 'exon file' formats (A=2 or A=5)
Methods
next_resultDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
write_result
No description
Code
result_count
No description
Code
report_count
No description
Code
_will_handleDescriptionCode
Methods description
next_resultcode    nextTop
 Title   : next_result
 Usage   : my $result = $searchio->next_result;
 Function: Returns the next Result from a search
 Returns : Bio::Search::Result::ResultI object
 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
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: Handle 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
_will_handlecodeprevnextTop
 Title   : _will_handle
 Usage   : Private method. For internal use only.
              if( $self->_will_handle($type) ) { ... }
 Function: Provides an optimized way to check whether or not an element of a 
           given type is to be handled.
 Returns : Reference to EventHandler object if the element type is to be handled.
           undef if the element type is not to be handled.
 Args    : string containing type of element.
Optimizations:
  1. Using the cached pointer to the EventHandler to minimize repeated lookups.
  2. Caching the will_handle status for each type that is encountered
     so that it only need be checked by calling handler->will_handle($type) once.
This does not lead to a major savings by itself (only 5-10%).
In combination with other optimizations, or for large parse jobs, the
savings good be significant.
To test against the unoptimized version, remove the parentheses from
around the third term in the ternary " ? : " operator and add two
calls to $self->_eventHandler().
Methods code
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    local $/ = "\n";
    local $_;

    # Declare/adjust needed variables
    $self->{'_last_data'} = '';
    my ($seentop, $qfull, @hsps, %alignment, $format);
    my $hit_direction = 1;

    # Start document and main element
    $self->start_document();
    $self->start_element({'Name' => 'Sim4Output'});
    my $lastquery = '';
    # Read output report until EOF
    while( defined($_ = $self->_readline) ) {       
        # Skip empty lines, chomp filled ones
	next if( /^\s+$/); chomp;

        # Make sure sim4 output format is not 2 or 5
        if (!$seentop) {
	    if ( /^\#:lav/ ) { $format = 2; }
            elsif ( /^<|>/ ) { $format = 5; }
            $self->throw("Bio::SearchIO::sim4 module cannot parse 'type $format' outputs.") if $format;
	}

        # This line indicates the start of a new hit
	if( /^seq1\s*=\s*(\S+),\s+(\d+)/ ) {
	    my ($nm,$desc) = ($1,$2);
            # First hit? Adjust some parameters if so
	    if ( ! $seentop ) {
	        $self->element( {'Name' => 'Sim4Output_query-def', 
				 'Data' => $nm} );
	        $self->element( {'Name' => 'Sim4Output_query-len', 
				 'Data' => $desc} );
                $seentop = 1;
	    } elsif( $nm ne $lastquery ) {
		$self->_pushback($_);
		last;
	    }
	    $lastquery = $nm;
            # A previous HSP may need to be ended
            $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
            # A previous hit exists? End it and reset needed variables
            if ( $self->in_element('hit') ) {
	        foreach (@hsps) {
                    $self->start_element({'Name' => 'Hsp'});
                    while (my ($name, $data) = each %$_) {
                        $self->{'_currentHSP'}{$name} = $data;
		    }
		    $self->end_element({'Name' => 'Hsp'});
                    $self->{'_currentHSP'} = {};
	        }
                $format = 0 if @hsps;
                @hsps = ();
                %alignment = ();
                $qfull = 0;
                $hit_direction = 1;
                $self->end_element({'Name' => 'Hit'});
	    }

        # This line describes the current hit... so let's start it
	} elsif( /^seq2\s*=\s*(\S+)\s+\(>?(\S+)\s*\),\s*(\d+)/ ) {
            $self->start_element({'Name' => 'Hit'});
	    $self->element( {'Name' => 'Hit_id', 'Data' => $2} );
	    $self->element( {'Name' => 'Hit_desc', 'Data' => $1} );
	    $self->element( {'Name' => 'Hit_len', 'Data' => $3} );

        # This line may give additional details about query or subject
	} elsif( /^>(\S+)\s*(.*)?/ ) {
            # Previous line was query details... this time subject details
	    if( $qfull )  {
                $format = 4 if !$format;
		$self->element({'Name' => 'Hit_desc', 'Data' => $2});
            # First line of this type is always query details for a given hit
	    } else { 
		$self->element({'Name' => 'Sim4Output_query-desc', 'Data' => $2});
		$qfull = 1;
	    }

        # This line indicates that subject is on reverse strand
	} elsif( /^\(complement\)/ ) {
	    $hit_direction = -1;

        # This line describes the current HSP... so add it to @hsps array
	} elsif( /^\(?(\d+)\-(\d+)\)?\s+\(?(\d+)\-(\d+)\)?\s+(\d+)/ ) {
		my ($qs,$qe,$hs,$he,$pid) = ($1,$2,$3,$4,$5);
                push @hsps, {
                    'Hsp_query-from' => $qs,
                    'Hsp_query-to' => $qe,
                    'Hsp_hit-from' => $hit_direction >= 0 ? $hs : $he,
                    'Hsp_hit-to' => $hit_direction >= 0 ? $he : $hs,
                    'Hsp_identity' => 0, #can't determine correctly from raw pct
                    'Hsp_qlength' => abs($qe - $qs) + 1,
                    'Hsp_hlength' => abs($he - $hs) + 1,
                    'Hsp_align-len' => abs($qe - $qs) + 1,
	        };

        # This line indicates the start of an alignment block
        } elsif( /^\s+(\d+)\s/ ) {
            # Store the current alignment block in a hash
	    for( my $i = 0; defined($_) && $i < 4; $i++ ) {
                my ($start, $string) = /^\s+(\d*)\s(.*)/;
                $alignment{$ALIGN_TYPES{$i}} = { start => $start, string => $i != 2
                    ? $string
                    : (' ' x (length($alignment{$ALIGN_TYPES{$i-1}}{string}) - length($string))) . $string
                };
                $_ = $self->_readline();
	    }

            # 'Ruler' line indicates the start of a new HSP
            if ($alignment{Ruler}{start} == 0) {
                $format = @hsps ? 3 : 1 if !$format;
                # A previous HSP may need to be ended
                $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
                # Start the new HSP and fill the '_currentHSP' property with available details
     	        $self->start_element({'Name' => 'Hsp'});
                $self->{'_currentHSP'} = @hsps ? shift @hsps : {
                    'Hsp_query-from' => $alignment{Query}{start},
                    'Hsp_hit-from' => $alignment{Sbjct}{start},
     	        }
	    }

            # Midline indicates a boundary between two HSPs
	    if ( $alignment{Mid}{string} =~ /<|>/g ) {
                my ($hsp_start, $hsp_end);
                # Are we currently in an open HSP?
    	        if ( $self->in_element('hsp') ) {
                    # Find end pos, adjust 'gaps', 'seq' and 'midline' properties... then close HSP
                    $hsp_end = (pos $alignment{Mid}{string}) - 1;
                    $self->{'_currentHSP'}{'Hsp_querygaps'} +=
                        ($self->{'_currentHSP'}{'Hsp_qseq'} .= substr($alignment{Query}{string}, 0, $hsp_end)) =~ s/ /-/g;
                    $self->{'_currentHSP'}{'Hsp_hitgaps'} +=
                        ($self->{'_currentHSP'}{'Hsp_hseq'} .= substr($alignment{Sbjct}{string}, 0, $hsp_end)) =~ s/ /-/g;
                    ($self->{'_currentHSP'}{'Hsp_midline'} .= substr($alignment{Mid}{string}, 0, $hsp_end)) =~ s/-/ /g;
                    $self->end_element({'Name' => 'Hsp'});

                    # Does a new HSP start in the current alignment block?
                    if ( $alignment{Mid}{string} =~ /\|/g ) {
                        # Find start pos, start new HSP and fill it with available details
                        $hsp_start = (pos $alignment{Mid}{string}) - 1;
                        $self->start_element({'Name' => 'Hsp'});
                        $self->{'_currentHSP'} = @hsps ? shift @hsps : {};
                        $self->{'_currentHSP'}{'Hsp_querygaps'} +=
                            ($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g;
                        $self->{'_currentHSP'}{'Hsp_hitgaps'} +=
                            ($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g;
                        ($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g;
		    }
		}
                # No HSP is currently open...
                else {
                    # Find start pos, start new HSP and fill it with available
                    # details then skip to next alignment block
		    $hsp_start = index($alignment{Mid}{string}, '|');
	            $self->start_element({'Name' => 'Hsp'});
                    $self->{'_currentHSP'} = @hsps ? shift @hsps : {
                        'Hsp_query-from' => $alignment{Query}{start},
    	            };
                    $self->{'_currentHSP'}{'Hsp_querygaps'} +=
                        ($self->{'_currentHSP'}{'Hsp_qseq'} = substr($alignment{Query}{string}, $hsp_start)) =~ s/ /-/g;
                    $self->{'_currentHSP'}{'Hsp_hitgaps'} +=
                        ($self->{'_currentHSP'}{'Hsp_hseq'} = substr($alignment{Sbjct}{string}, $hsp_start)) =~ s/ /-/g;
                    ($self->{'_currentHSP'}{'Hsp_midline'} = substr($alignment{Mid}{string}, $hsp_start)) =~ s/-/ /g;
                    next;
		}
	    }
            # Current alignment block does not contain HSPs boundary
            else {
                # Start a new HSP if none is currently open
	        # (Happens if last boundary finished at the very end of previous block)
	        if ( !$self->in_element('hsp') ) {
     	            $self->start_element({'Name' => 'Hsp'});
                    $self->{'_currentHSP'} = @hsps ? shift @hsps : {
                        'Hsp_query-from' => $alignment{Query}{start},
                        'Hsp_hit-from' => $alignment{Sbjct}{start},
     	            }
		}
                # Adjust details of the current HSP
                $self->{'_currentHSP'}{'Hsp_query-from'} ||= 
		    $alignment{Query}{start} - 
		    length($self->{'_currentHSP'}{'Hsp_qseq'} || '');
                $self->{'_currentHSP'}{'Hsp_hit-from'} ||= 
		    $alignment{Sbjct}{start} - 
		    length($self->{'_currentHSP'}{'Hsp_hseq'} || '');
                $self->{'_currentHSP'}{'Hsp_querygaps'} +=
                    ($self->{'_currentHSP'}{'Hsp_qseq'} .= 
		     $alignment{Query}{string}) =~ s/ /-/g;
                $self->{'_currentHSP'}{'Hsp_hitgaps'} +=
                    ($self->{'_currentHSP'}{'Hsp_hseq'} .= 
		     $alignment{Sbjct}{string}) =~ s/ /-/g;
                ($self->{'_currentHSP'}{'Hsp_midline'} .= 
		 $alignment{Mid}{string}) =~ s/-/ /g;
	    }
	}
    }

    # We are done reading the sim4 report, end everything and return
    if( $seentop ) {
        # end HSP if needed
        $self->end_element({'Name' => 'Hsp'}) if ( $self->in_element('hsp') );
        # end Hit if needed
        if ( $self->in_element('hit') ) {
            foreach (@hsps) {
                $self->start_element({'Name' => 'Hsp'});
                while (my ($name, $data) = each %$_) {
                    $self->{'_currentHSP'}{$name} = $data;
    	        }
    	        $self->end_element({'Name' => 'Hsp'});
            }
            $self->end_element({'Name' => 'Hit'});
	}
        # adjust result's algorithm name, end output and return
        $self->element({'Name' => 'Sim4Output_program',
                        'Data' => $DEFAULTFORMAT . ' (A=' . (defined $format ? $format : '?') . ')'});
	$self->end_element({'Name' => 'Sim4Output'});
	return $self->end_document();
    } 
    return;
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($self,$data) = @_;
   # we currently don't care about attributes
   my $nm = $data->{'Name'};
   my $type = $MODEMAP{$nm};

   if( $type ) {
       if( $self->_will_handle($type) ) {
	   my $func = sprintf("start_%s",lc $type);
	   $self->_eventHandler->$func($data->{'Attributes'});
       }
       unshift @{$self->{'_elements'}}, $type;

       if($type eq 'result') {
	   $self->{'_values'} = {};
	   $self->{'_result'}= undef;
       }
   }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    my $rc;
    
    if( $nm eq 'Hsp' ) {
        $self->{'_currentHSP'}{'Hsp_midline'} ||= '';
	$self->{'_currentHSP'}{'Hsp_query-to'} ||=
            $self->{'_currentHSP'}{'Hsp_query-from'} + length($self->{'_currentHSP'}{'Hsp_qseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_querygaps'};
        $self->{'_currentHSP'}{'Hsp_hit-to'} ||=
            $self->{'_currentHSP'}{'Hsp_hit-from'} + length($self->{'_currentHSP'}{'Hsp_hseq'}) - 1 - $self->{'_currentHSP'}{'Hsp_hitgaps'};
        $self->{'_currentHSP'}{'Hsp_identity'} ||= 
	    ($self->{'_currentHSP'}{'Hsp_midline'} =~ tr/\|//);
        $self->{'_currentHSP'}{'Hsp_qlength'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1;
        $self->{'_currentHSP'}{'Hsp_hlength'} ||= abs($self->{'_currentHSP'}{'Hsp_hit-to'} - $self->{'_currentHSP'}{'Hsp_hit-from'}) + 1;
        $self->{'_currentHSP'}{'Hsp_align-len'} ||= abs($self->{'_currentHSP'}{'Hsp_query-to'} - $self->{'_currentHSP'}{'Hsp_query-from'}) + 1;
        $self->{'_currentHSP'}{'Hsp_score'} ||= int(100 * ($self->{'_currentHSP'}{'Hsp_identity'} / $self->{'_currentHSP'}{'Hsp_align-len'}));
        foreach (keys %{$self->{'_currentHSP'}}) {
            $self->element({'Name' => $_, 'Data' => delete ${$self->{'_currentHSP'}}{$_}});
	}
    }

    if( $type = $MODEMAP{$nm} ) {
	if( $self->_will_handle($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 $rc;
}
elementdescriptionprevnextTop
sub element {
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$data) = @_;
   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
   
   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  

   $self->{'_last_data'} = $data->{'Data'};
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($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->{'_elements'} = [];
    $self->{'_reporttype'} = $DEFAULTFORMAT;
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
write_resultdescriptionprevnextTop
sub write_result {
   my ($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( $blast, @args );
}
result_countdescriptionprevnextTop
sub result_count {
    return 1; # can a sim4 report contain more than one result?
}
report_countdescriptionprevnextTop
sub report_count {
 shift->result_count
}
_will_handledescriptionprevnextTop
sub _will_handle {
    my ($self,$type) = @_;
    my $handler = $self->{'_handler_cache'} ||= $self->_eventHandler;

    my $will_handle = defined($self->{'_will_handle_cache'}->{$type})
                             ? $self->{'_will_handle_cache'}->{$type}
                             : ($self->{'_will_handle_cache'}->{$type} =
                               $handler->will_handle($type));

    return $will_handle ? $handler : undef;
}
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/wiki/Mailing_lists  - 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.open-bio.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
CONTRIBUTORSTop
Luc Gauthier (lgauthie@hotmail.com)
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::sim4();
 Function: Builds a new Bio::SearchIO::sim4 object
 Returns : an instance of Bio::SearchIO::sim4
 Args    :