view release on metacpan or  search on metacpan

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

 return unless $self->mode eq 'r'; # returns if can't read next_feature when we're in write mode

 while ( my $line = $self->_readline() ) {
   chomp $line;
   if ( $line =~ /^>Vector (\S+)/ ) {
     $self->{parse_state}{seqname} = $1;
   } elsif ( $line =~ /^\s*WARNING/ ) {
     $self->warn("$self->{parse_state}{seqname}: vecscreen says: $line\n");
   } elsif ( $line =~ /\S/ ) {

     $self->{parse_state}{seqname}
	or $self->throw("Unexpected line in vecscreen output '$line'");

     #if it's not a vector line, it should be either a match type or
     #a coordinates line
     my $lcline = lc $line;

     if ( $line =~ /^(\d+)\s+(\d+)\s*$/ ) {
	my ($s,$e) = ($1,$2);

	my $matchtype = $self->{parse_state}{matchtype};
	$matchtype =~ s/\s/_/g; #replace whitespace with underscores for the primary tag
	return Bio::SeqFeature::Generic->new( -start    => $s,
					      -end      => $e,
					      -primary  => $matchtype,
					      -seq_id   => $self->{parse_state}{seqname},
					    );
     } elsif ( $lcline eq 'no hits found' ) {
	$self->{parse_state}{seqname} = '';
     } elsif ( grep $lcline eq $_, 'strong match', 'moderate match', 'weak match', 'suspect origin') {
	$self->{parse_state}{matchtype} = $lcline;
     } else {
	$self->throw("Parse error.  Expected a match type or coordinate line but got '$line'");
     }
   } else {
     #blank line, ignore it and reset parser

     $self->{parse_state}{seqname} = ''; #< a line with whitespace
     #indicates a boundary
     #between output for
     #different sequences
     $self->{parse_state}{matchtype} = '';
   }
 }

 return;
}

=head2 write_feature (NOT IMPLEMENTED)

  Title   : write_feature
  Usage   : $io->write_feature($feature)
  Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format
  Example :
  Args    : Bio::SeqFeatureI object
  Returns :

=cut

sub write_feature {
 shift->throw_not_implemented;
}


###
1;#do not remove
###