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Bio/Tools/EPCR.pm  view on Meta::CPAN

 Returns : Bio::Tools::EPCR
 Args    : -fh   => filehandle
           OR
           -file => filename

           -primary => a string to be used as the common value for
                       each features '-primary' tag.  Defaults to
                       'sts'.  (This in turn maps to the GFF 'type'
                       tag (aka 'method')).

            -source => a string to be used as the common value for
                       each features '-source' tag.  Defaults to
                       'e-PCR'. (This in turn maps to the GFF 'source'
                       tag)

             -groupclass => a string to be used as the name of the tag
                           which will hold the sts marker namefirst
                           attribute.  Defaults to 'name'.

=cut

sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($primary, $source, 
      $groupclass) = $self->_rearrange([qw(PRIMARY
					   SOURCE 
					   GROUPCLASS)],@args);
  $self->primary(defined $primary ? $primary : 'sts');
  $self->source(defined $source ? $source : 'e-PCR');
  $self->groupclass(defined $groupclass ? $groupclass : 'name');

  $self->_initialize_io(@args);
  return $self;
}

=head2 next_feature

 Title   : next_feature
 Usage   : $seqfeature = $obj->next_feature();
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none    

=cut

sub next_feature {
    my ($self) = @_;
    my $line = $self->_readline;
    return unless defined($line);
    chomp($line);
    my($seqname,$location,$mkrname, $rest) = split(/\s+/,$line,4);
    
    my ($start,$end) = ($location =~ /(\S+)\.\.(\S+)/);

    # `e-PCR -direct` results code match strand in $rest as (+) and (-).  Decode it if present.
    my $strandsign;
    if ($rest =~ m/^\(([+-])\)(.*)$/) {
      ($strandsign,$rest) = ($1, $2);
    } else {
      $strandsign = "?";
    }
    my $strand = $strandsign eq "+" ? 1 :  $strandsign eq "-" ? -1 : 0;

    my $markerfeature = Bio::SeqFeature::Generic->new 
	( '-start'   => $start,
	  '-end'     => $end,
	  '-strand'  => $strand,
	  '-source'  => $self->source,
	  '-primary' => $self->primary,
	  '-seq_id'  => $seqname,
	  '-tag'     => {
	      $self->groupclass => $mkrname,
	      ($rest ? ('Note'            => $rest ) : ()),
	  });
    #$markerfeature->add_tag_value('Note', $rest) if defined $rest;
    return $markerfeature;
}

=head2 source

 Title   : source
 Usage   : $obj->source($newval)
 Function: 
 Example : 
 Returns : value of source (a scalar)
 Args    : on set, new value (a scalar or undef, optional)


=cut

sub source{
    my $self = shift;
    return $self->{'_source'} = shift if @_;
    return $self->{'_source'};
}

=head2 primary

 Title   : primary
 Usage   : $obj->primary($newval)
 Function: 
 Example : 
 Returns : value of primary (a scalar)
 Args    : on set, new value (a scalar or undef, optional)


=cut

sub primary{
    my $self = shift;
    return $self->{'_primary'} = shift if @_;
    return $self->{'_primary'};
}

=head2 groupclass

 Title   : groupclass
 Usage   : $obj->groupclass($newval)
 Function: 
 Example : 
 Returns : value of groupclass (a scalar)
 Args    : on set, new value (a scalar or undef, optional)