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lib/Bio/Polloc/LocusIO/gff3.pm  view on Meta::CPAN

   my($self,$value) = @_;
   return unless defined $value;
   if(ref($value) && ref($value) =~ m/array/i){
      my $out = "";
      for my $att (@{$value}){
	 $out.= "," . $self->_gff3_value($att);
      }
      $out = substr($out, 1) if $out;
      return $out;
   }
   return $self->_gff3_value($value);
}

=head2 _gff3_value

Properly escapes a value on the GFF3 line.  I.e., the content of one column.
Not to be used with the ninth column, because scapes the colon. the comma and
the equals signs.  Use instead the L<_gff3_attribute> function attribute by
attribute

=head3 Purpose

To simplify the code of L<gff3_line>

=head3 Arguments

The value to escape

=head3 Returns

The escaped value

=cut

sub _gff3_value {
   my ($self,$value) = @_;
   return unless defined $value;
   $value =~ s/%/%25/g;
   $value =~ s/\{\{%25\}\}/%/g;
   $value =~ s/\t/%9/g;
   $value =~ s/\n/\%D/g;
   $value =~ s/\r/\%A/g;
   $value =~ s/;/%3B/g;
   $value =~ s/=/%3D/g;
   $value =~ s/&/%26/g;
   $value =~ s/,/%2C/g;
   $value =~ s/ /%20/g;
   return $value;
}

=head2 _gff_decode

Decodes the URI-fashioned values on GFF3

=head3 Arguments

The value to decode (str)

=head3 Returns

The decoded value (str)

=cut

sub _gff3_decode {
   my($self,$value) = @_;
   return unless defined $value;
   $value =~ s/%25/%/g;
   $value =~ s/%9/\t/g;
   $value =~ s/\%D/\n/g;
   $value =~ s/\%A/\r/g;
   $value =~ s/%3B/;/g;
   $value =~ s/%3D/=/g;
   $value =~ s/%26/&/g;
   $value =~ s/%2C/,/g;
   $value =~ s/%20/ /g;
   return $value;
}

1;