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Summary

Bio::Search::HSP::FastaHSP - HSP object for FASTA specific data

Package variables

Included modules

Inherit

Bio::Search::HSP::GenericHSP

Synopsis

  # get a FastaHSP from a SearchIO stream
  my $in = new Bio::SearchIO(-format => 'fasta', -file => 'filename.fasta');

  while( my $r = $in->next_result) {
      while( my $hit = $r->next_result ) {
           while( my $hsp = $hit->next_hsp ) {
              print "smith-waterman score (if available): ", 
                    $hsp->sw_score(),"\n";
           }
      }
  }

Description

Describe the object here

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Search::HSP::FastaHSP();
 Function: Builds a new Bio::Search::HSP::FastaHSP object 
 Returns : Bio::Search::HSP::FastaHSP
 Args    : -swscore => smith-waterman score

 Title   : sw_score
 Usage   : $obj->sw_score($newval)
 Function: Get/Set Smith-Waterman score
 Returns : value of sw_score
 Args    : newvalue (optional)

Methods code

sub get_aln {

    my ($self) = @_;
    require Bio::LocatableSeq;
    require Bio::SimpleAlign;
    my $aln = new Bio::SimpleAlign;
    my $hs = $self->hit_string();
    my $qs = $self->query_string();

    # fasta reports some extra 'regional' sequence information
    # we need to clear out first
    # this seemed a bit insane to me at first, but it appears to 
    # work --jason
    
    # we infer the end of the regional sequence where the first
    # non space is in the homology string
    # then we use the HSP->length to tell us how far to read
    # to cut off the end of the sequence
        
    my ($start) = 0;
    if( $self->homology_string() =~ /^(\s+)/ ) {
	$start = CORE::length($1);
    }
    $self->debug("hs seq is '$hs'\n");
    $self->debug("qs seq is '$qs'\n");
	

    $hs = substr($hs, $start,$self->length('total'));
    $qs = substr($qs, $start,$self->length('total'));
    foreach my $seq ( $qs,$hs)  {
	foreach my $f ( '\\', '/', ' ') {
	    my $index =  index($seq,$f);
	    while( $index >=0 && length($seq) > 0 ) {
		substr($hs,$index,1) = '';
		substr($qs,$index,1) = '';
		$self->debug( "$f, $index+1, for ".length($seq). " ($seq)\n");
		$index = index($seq,$f,$index+1);
	    }
	}
    }

    my $seqonly = $qs;
    $seqonly =~ s/[\-\s]//g;
    my ($q_nm,$s_nm) = ($self->query->seq_id(),
			$self->hit->seq_id());
    unless( defined $q_nm && CORE::length ($q_nm) ) {
	$q_nm = 'query';
    }
    unless( defined $s_nm && CORE::length ($s_nm) ) {
	$s_nm = 'hit';
    }
    my $query = new Bio::LocatableSeq('-seq'   => $qs,
				      '-id'    => $q_nm,
				      '-start' => 1,
				      '-end' => CORE::length($seqonly),
				      );
    $seqonly = $hs;
    $seqonly =~ s/[\-\s]//g;
    my $hit =  new Bio::LocatableSeq('-seq'   => $hs,
				      '-id'    => $s_nm,
				      '-start' => 1,
				      '-end' => CORE::length($seqonly),
				      );
    $aln->add_seq($query);
    $aln->add_seq($hit);
    return $aln;
}


1;

}

sub new {

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

  my $self = $class->SUPER::new(@args);
  
  my ($swscore) = $self->_rearrange([qw(SWSCORE)], @args);

  defined $swscore && $self->sw_score($swscore);

  return $self;

}

sub sw_score {

    my ($self,$value) = @_;
    if( defined $value || ! defined $self->{'_sw_score'} ) {
	$value = 0 unless defined $value; # default value
	$self->{'_sw_score'} = $value;
    }
    return $self->{'_sw_score'};

}

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://bugzilla.bioperl.org/

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 _