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lib/Bio/Variation/IO.pm  view on Meta::CPAN

=cut


sub new {
   my ($class, %param) = @_;
   my ($format);

   @param{ map { lc $_ } keys %param } = values %param;  # lowercase keys
   $format = $param{'-format'}
             || $class->_guess_format( $param{-file} || $ARGV[0] )
             || 'flat';
   $format = "\L$format"; # normalize capitalization to lower case

   return unless $class->_load_format_module($format);
   return "Bio::Variation::IO::$format"->new(%param);
}


=head2 format

lib/Bio/Variation/IO.pm  view on Meta::CPAN

    my ($self, $seq) = @_;
    $self->throw("Sorry, you cannot write to a generic Bio::Variation::IO object.");
}

sub write_seq {
   my ($self, $seq) = @_;
   $self->warn("These are not sequence objects. Use method 'write' instead of 'write_seq'.");
   $self->write($seq);
}

=head2 _guess_format

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :

=cut

sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'flat'     if /\.dat$/i;
   return 'xml'     if /\.xml$/i;
}


1;