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lib/Bio/FeatureIO/ptt.pm  view on Meta::CPAN

 Returns : Bio::SeqFeatureI object

=cut

sub next_feature {
  my $self = shift;
  $self->mode eq 'r' || return; # returns if can't read next_feature when we're in write mode
  
  my $line = $self->_readline() or return; # returns if end of file, no more features?
  chomp $line;
  my @col = split m/\t/, $line;
  @col==$NUM_COL or $self->throw("Too many columns for PTT line");

  $col[0] =~ m/(\d+)\.\.(\d+)/ or $self->throw("Invalid location (column 1)");
  my $feat = Bio::SeqFeature::Generic->new(-start=>$1, -end=>$2, -primary=>'CDS');
  $col[1] =~ m/^([+-])$/ or $self->throw("Invalid strand (column 2)");
  $feat->strand($1 eq '+' ? +1 : -1);
  for my $i (2 .. $NUM_COL-1) {
    $feat->add_tag_value($NAME_OF{$i}, $col[$i]) if $col[$i] ne '-';
  }
  return $feat;