Summary

Bio::SearchIO::fasta - A SearchIO parser for FASTA results

Package variables

Included modules

Inherit

Bio::SearchIO

Synopsis

  # Do not use this object directly, use it through the SearchIO system
   use Bio::SearchIO;
   my $searchio = new Bio::SearchIO(-format => 'fasta',
				    -file   => 'report.FASTA');
   while( my $result = $searchio->next_result ) {
	# ....
   }

Description

This object contains the event based parsing code for FASTA format reports.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::fasta();
 Function: Builds a new Bio::SearchIO::fasta object 
 Returns : Bio::SearchIO::fasta
 Args    :

 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

 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'

 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'

 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'

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

 Title   : _mode
 Usage   : $obj->_mode($newval)
 Function: 
 Example : 
 Returns : value of _mode
 Args    : newvalue (optional)

 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

 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

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

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

Methods code

BEGIN {

     # mapping of NCBI Blast terms to Bioperl hash keys
    %MODEMAP = ('FastaOutput' => 'result',
		'Hit'         => 'hit',
		'Hsp'         => 'hsp'
		);

    # This should really be done more intelligently, like with
    # XSLT

    %MAPPING = ( 
		 'Hsp_bit-score' => 'bits',
		 'Hsp_score'     => 'score',
		 'Hsp_sw-score'  => 'swscore',
		 'Hsp_evalue'    => 'evalue',
		 'Hsp_query-from'=> 'querystart',
		 'Hsp_query-to'  => 'queryend',
		 'Hsp_hit-from'  => 'hitstart',
		 'Hsp_hit-to'    => 'hitend',
		 'Hsp_positive'  => 'conserved',
		 'Hsp_identity'  => 'identical',
		 'Hsp_gaps'      => 'gaps',
		 'Hsp_hitgaps'   => 'hitgaps',
		 'Hsp_querygaps' => 'querygaps',
		 'Hsp_qseq'      => 'queryseq',
		 'Hsp_hseq'      => 'hitseq',
		 'Hsp_midline'   => 'homolseq',
		 'Hsp_align-len' => 'hsplen',
		 'Hsp_query-frame'=> 'queryframe',
		 'Hsp_hit-frame'  => 'hitframe',

		 'Hit_id'        => 'hitname',
		 'Hit_len'       => 'hitlen',
		 'Hit_accession' => 'hitacc',
		 'Hit_def'       => 'hitdesc',
		 'Hit_signif'    => 'hitsignif',
		 'Hit_score'     => 'hitscore',
		 
		 'FastaOutput_program'  => 'programname',
		 'FastaOutput_version'  => 'programver',
		 'FastaOutput_query-def'=> 'queryname',
		 'FastaOutput_query-len'=> 'querylen',
		 'FastaOutput_db'       => 'dbname',
		 'FastaOutput_db-len'   => 'dbsize',
		 'FastaOutput_db-let'   => 'dblets',

		 'Parameters_matrix'    => { 'param' => 'matrix'},
		 'Parameters_expect'    => { 'param' => 'expect'},
		 'Parameters_include'   => { 'param' => 'include'},
		 'Parameters_sc-match'  => { 'param' => 'match'},
		 'Parameters_sc-mismatch' => { 'param' => 'mismatch'},
		 'Parameters_gap-open'  => { 'param' => 'gapopen'},
		 'Parameters_gap-ext'   => { 'param' => 'gapext'},
		 'Parameters_word-size' => { 'param' => 'wordsize'},
		 'Parameters_ktup'      => { 'param' => 'ktup'},
		 'Parameters_filter'    => {'param' => 'filter'},
		 'Statistics_db-num'    => { 'stat' => 'dbentries'},
		 'Statistics_db-len'    => { 'stat' => 'dbletters'},
		 'Statistics_hsp-len'   => { 'stat' => 'hsplength'},
		 'Statistics_eff-space' => { 'stat' => 'effectivespace'},
		 'Statistics_kappa'     => { 'stat' => 'kappa' },
		 'Statistics_lambda'    => { 'stat' => 'lambda' },
		 'Statistics_entropy'   => { 'stat' => 'entropy'},
		 );

}

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

}

sub next_result {

   my ($self) = @_;
   
   my $data = '';
   my $seentop = 0;
   
   $self->start_document();
   my @hit_signifs;
   while( defined ($_ = $self->_readline )) {       
       next if( ! $self->in_element('hsp')  &&
		/^\s+$/); # skip empty lines
       if( /(\S+)\s+searches\s+a\s+((protein\s+or\s+DNA\s+sequence)|(sequence\s+database))/i || /(\S+) compares a/ ) {
	   if( $seentop ) {
	       $self->_pushback($_);
	       $self->end_element({ 'Name' => 'FastaOutput'});
	       return $self->end_document();
	   }
	   $self->{'_reporttype'} = $1;
	   $self->start_element({ 'Name' => 'FastaOutput' } );
	   $seentop = 1;
	   
	   $self->element({ 'Name' => 'FastaOutput_program',
			    'Data' => $self->{'_reporttype'}});
	   $_ = $self->_readline();
	   my ($version) = (/version\s+(\S+)/);
	   $version = '' unless defined $version;
	   $self->element({ 'Name' => 'FastaOutput_version',
			    'Data' => $version});
	   my ($last);
	   while( defined($_ = $self->_readline()) ) {
	       if( /\s+>(.+)/ || /^\s*vs\s+/ ) {
		   my $querydef = $1;
		   
		   if( $last =~ /(\S+)[:,]\s*(\d+)\s+(aa|nt)/ ) {
		       if( $self->{'_reporttype'} &&
			   $self->{'_reporttype'} eq 'FASTA' ) {
			   if( $3 eq 'nt') {
			       $self->{'_reporttype'} = 'FASTN' ;
			   } elsif( $3 eq 'aa' ) {
			       $self->{'_reporttype'} = 'FASTP' ;
			   }
		       }
		       
		       $self->element({'Name' => 'FastaOutput_query-def',
				       'Data' => $querydef || $1});
		       $self->element({'Name' => 'FastaOutput_query-len',
				       'Data' => $2});
		   } else {
		       $self->element({'Name' => 'FastaOutput_query-def',
				       'Data' => $querydef });
		       $self->warn("unable to find and set query length");
		   }
		   last;
	       } 
	       $last = $_;
	   }

	   if( $last =~ /^\s*vs\s+(\S+)/ ||	       	       
	       (defined $_ && /^\s*vs\s+(\S+)/) ||
	       (defined ($_ = $self->_readline()) && /^\s*vs\s+(\S+)/)
	       ) {
	       $self->element({'Name' => 'FastaOutput_db',
			       'Data' => $1});
	   }
       } elsif( /(\d+) residues in\s+(\d+)\s+sequences/ ) {
	   $self->element({'Name' => 'FastaOutput_db-let',
			   'Data' => $1});
	   $self->element({'Name' => 'FastaOutput_db-len',
			   'Data' => $2});
	   $self->element({'Name' => 'Statistics_db-len',
			   'Data' => $1});
	   $self->element({'Name' => 'Statistics_db-num',
			   'Data' => $2});	   
       } elsif( /Lambda=\s+(\S+)/ ) {
	   $self->element({'Name' => 'Statistics_lambda',
			   'Data' => $1});	  
       } elsif( /^\s*(Smith-Waterman).+(\S+)\s*matrix/ ) {	   
	   $self->element({'Name' => 'Parameters_matrix',
			   'Data' => $2});
	   $self->{'_reporttype'} = $1;

	   $self->element({ 'Name' => 'FastaOutput_program',
			    'Data' => $self->{'_reporttype'}});
	   
       } elsif( /The best scores are:/ ) {
	   while( defined ($_ = $self->_readline() ) && 
		  ! /^\s+$/ ) {	       
	       my @line = split;
	       # 0 is signif, 1 is raw score
	       push @hit_signifs, [ pop @line, pop @line];
	   }
	   
       } elsif( /^\s*([T]?FAST[XYAF]).+,\s*(\S+)\s*matrix.+ktup:\s*(\d+)/ ) {
	   $self->element({'Name' => 'Parameters_matrix',
			   'Data' => $2});
	   $self->element({'Name' => 'Parameters_ktup',
			   'Data' => $3});
	   $self->{'_reporttype'} = $1 if( $self->{'_reporttype'} !~ /FAST[PN]/i ) ;

	   $self->element({ 'Name' => 'FastaOutput_program',
			    'Data' => $self->{'_reporttype'}});
	   
       } elsif( /gap\-pen:\s+([\-\+]?\d+)\/\s+([\-\+]?\d+).+width:\s+(\d+)/ ) {
	   $self->element({'Name' => 'Parameters_gap-open',
			   'Data' => $1});
	   $self->element({'Name' => 'Parameters_gap-ext',
			   'Data' => $2});
	   $self->element({'Name' => 'Parameters_word-size',
			   'Data' => $3});
       } elsif( /^>>(.+) \((\d+)\s*(aa|nt)\)$/ ) {
	   if( $self->in_element('hsp') ) {
	       $self->end_element({ 'Name' => 'Hsp'});
	   }
	   if( $self->in_element('hit') ) {
	       $self->end_element({ 'Name' => 'Hit'});
	   }
	   
	   $self->start_element({'Name' => 'Hit'});
	   $self->element({ 'Name' => 'Hit_len',
			    'Data' => $2});  
	   my ($id,$desc) = split(/\s+/,$1,2);
	   $self->element({ 'Name' => 'Hit_id',
			    'Data' => $id}); 	   
	   my $v = shift @hit_signifs;
	   if( defined $v ) {
	       $self->element({'Name' => 'Hit_signif',
			       'Data' => $v->[0]});
	       $self->element({'Name' => 'Hit_score',
			       'Data' => $v->[1]});
	   }
	   my @pieces = split(/\|/,$id);
	   my $acc = pop @pieces;
	   $acc =~ s/\.\d+$//;
	   $self->element({ 'Name' =>  'Hit_accession',
			    'Data'  => $acc});	
	   $self->element({ 'Name' => 'Hit_def',
			    'Data' => $desc});	   
	   $self->start_element({'Name' => 'Hsp'});
	   $_ = $self->_readline();
	   my ($score,$bits,$e) = ( /Z-score:\s*(\S+)\s*bits:\s*(\S+)\s+E\(\):\s*(\S+)/ );
	   $self->element({'Name' => 'Hsp_score',
			   'Data' => $score});
	   $self->element({'Name' => 'Hsp_evalue',
			   'Data' => $e});
	   $self->element({'Name' => 'Hsp_bit-score',
			   'Data' => $bits});
	   $_ = $self->_readline();
	   if( /Smith-Waterman score:\s*(\d+)/ ) {
	       $self->element({'Name' => 'Hsp_sw-score',
			       'Data' => $1});
	   }
	   if( /(\d+\.\d+)\%\s*identity\s*\((\d+\.\d+)\%\s*ungapped\)\s*in\s*(\d+)\s+(aa|nt)\s+overlap\s*\((\d+)\-(\d+):(\d+)\-(\d+)\)/ ) {
	       my ($identper,$gapper,$len,$querystart,
		   $queryend,$hitstart,$hitend) = ($1,$2,$3,$5,$6,$7,$8);
	       my $ident = POSIX::ceil(($identper/100) * $len);
	       my $gaps = POSIX::ceil ( ($gapper/100) * $len);
	       
	       $self->element({'Name' => 'Hsp_gaps',
			       'Data' => $gaps});
	       $self->element({'Name' => 'Hsp_identity',
			       'Data' => $ident});
	       $self->element({'Name' => 'Hsp_positive',
			       'Data' => $ident});
	       $self->element({'Name' => 'Hsp_align-len',
			       'Data' => $len});
	       
	       $self->element({'Name' => 'Hsp_query-from',
			       'Data' => $querystart});
	       $self->element({'Name' => 'Hsp_query-to',
			       'Data' => $queryend});
	       $self->element({'Name' => 'Hsp_hit-from',
			       'Data' => $hitstart});
	       $self->element({'Name' => 'Hsp_hit-to',
			       'Data' => $hitend});
	   } else {
	       $self->warn( "unable to parse FASTA score line: $_");
	   }
       } elsif( /\d+\s*residues\s*in\s*\d+\s*query\s*sequences/ ) {
	   if( $self->in_element('hsp') ) {
	       $self->end_element({'Name' => 'Hsp'});
	   } 
	   if( $self->in_element('hit') ) {
	       $self->end_element({'Name' => 'Hit'});
	   }
	   
#	   $_ = $self->_readline();
#	   my ( $liblen,$libsize) = /(\d+)\s+residues\s*in(\d+)\s*library/;
	   # fast forward to the end of the file as there is 
	   # nothing else left to do with this file and want to be sure and
	   # reset it
	   while(defined($_ = $self->_readline() ) ) { 
	       last if( /^Function used was/);
	       if( /(\S+)\s+searches\s+a\s+(protein\s+or\s+DNA\s+sequence)|(sequence\s+database)/ ) { 
		   $self->_pushback($_);
	       }
	   }
	   $self->end_element({ 'Name' => 'FastaOutput'});
	   return $self->end_document();
       } elsif( $self->in_element('hsp' ) ) {
	   
	   my @data = ( '','','');
	   my $count = 0;
	   my $len = 0;
	   
	   while( defined($_ ) ) {
	       chomp;
	       if( /residues in \d+\s+query\s+sequences/) {
		   $self->_pushback($_);
		   last;
	       }
	       if( $count == 0 ) {
	       } elsif( $count == 1 || $count == 3 ) {
		   if( /^(\S+\s+)(\S+)/ ) {
		       $len = length($1);
		       $data[$count-1] = $2;
		   } elsif( /^\s+\d+/ ) {
		       $count--; # handle the case where we're off by one line
		   } elsif( /^\s+/ || length($_) == 0) {
		       
		   } else {
		       $self->warn("Unrecognized alignment line ($count) $_");
		   }
	       } elsif( $count == 2 ) {		   
		   # toss the first 7 characters of the line
		   if( length($_) >= $len ) {
		       $data[$count-1] = substr($_,$len);
		   }
	       } 
	       	       
	       last if( $count++ >= 5);
	       $_ = $self->_readline();	       
	   }
	   if( length($data[0]) > 0 ) {
	       $self->characters({'Name' => 'Hsp_qseq',
				  'Data' => $data[0] });
	       $self->characters({'Name' => 'Hsp_midline',
				  'Data' => $data[1]});
	       $self->characters({'Name' => 'Hsp_hseq',
				  'Data' => $data[2]});
	   }
       } else {
	   if( ! $seentop ) {
	       print;
	       
	       $self->warn("unrecognized FASTA Family report file!");
	       return undef;
	   }
       }
   }

}

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 'FastaOutput') {
	$self->{'_values'} = {};
	$self->{'_result'}= undef;
	$self->{'_mode'} = '';
    }

}

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( $nm eq 'Hsp' ) {
	foreach ( qw(Hsp_qseq Hsp_midline Hsp_hseq) ) {
	    $self->element({'Name' => $_,
			    'Data' => $self->{'_last_hspdata'}->{$_}});
	}
	$self->{'_last_hspdata'} = {}
    }

    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 { 
	print "unknown nm $nm, ignoring\n";
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
				# end of an element
    $self->{'_result'} = $rc if( $nm eq 'FastaOutput' );
    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'} && $data->{'Data'} !~ /^\s+$/ );

   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
       
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  
   
   $self->{'_last_data'} = $data->{'Data'};

}

sub _mode {

    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_mode'} = $value;
    }
    return $self->{'_mode'};

}

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->{'_mode'} = '';
    $self->{'_elements'} = [];

}

sub end_document {

   my ($self,@args) = @_;
   return $self->{'_result'};

}

General documentation

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

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
email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

Email jason@bioperl.org
Describe contact details here

Additional contributors names and emails here

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