view release on metacpan or  search on metacpan

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

                                              -format => 'generic'       );
 Args    : -file : Path of a community file. See file() in Bio::Root::IO.
           -format : Format of the file, either 'generic', 'biom', 'gaas',
               'qiime' or 'unifrac'. This is optional when reading a community
               file because the format is automatically detected by the
               Bio::Community::IO::FormatGuesser module. See also format() in
               Bio::Root::IO.
           -weight_files : Arrayref of files (or filehandles) that contain
               weights to assign to members. See weight_files().
           -weight_assign : When using files of weights, define what to do for
               community members that do not have weights. See weight_assign().
           -taxonomy: Given a Bio::DB::Taxonomy object, try to place the community
               members in this taxonomy. See taxonomy().
           -skip_empty_communities: Skip communities with no members. See
               skip_empty_communities()
           See the documentation for _initialize_io() in Bio::Root::IO for other
           accepted constructors like -fh, -string, -input, or -url.
 Returns : A Bio::Community::IO object

=cut


package Bio::Community::IO;

use Moose;
use Moose::Util qw/does_role/;
use MooseX::NonMoose;
use namespace::autoclean;
use Module::Runtime;
use Method::Signatures;
use Bio::Community;
use Bio::Community::Meta;
use Bio::Community::Types;
use Bio::Community::IO::FormatGuesser;
use Bio::Community::TaxonomyUtils
   qw(split_lineage_string get_taxon_lineage get_lineage_string clean_lineage_arr);

extends 'Bio::Root::Root',
        'Bio::Root::IO';


has '_meta' => (
   is => 'rw',
   #isa => undef, # Bio::Community::Meta
   required => 0,
   init_arg => undef,
   default => undef,
   lazy => 1,
);


# Overriding new... Is there a better alternative?

func new ($class, @args) {
   my $real_class = Scalar::Util::blessed($class) || $class;

   # These all come from the same base, Moose::Object, so this is fine
   my $params = $real_class->BUILDARGS(@args);
   my $format = delete $params->{'-format'};
   if (not defined $format) {
      # Try to guess format
      my $guesser = Bio::Community::IO::FormatGuesser->new();
      if ($params->{'-file'}) {
         $guesser->file( $params->{'-file'} );
      } elsif ($params->{'-fh'}) {
         $guesser->fh( $params->{'-fh'} );
      }
      $format = $guesser->guess;
   }
   if (not defined $format) {
      $real_class->throw("Could not automatically detect input format.");
   }

   # Use the real driver class here
   $real_class = __PACKAGE__.'::Driver::'.$format;
   Module::Runtime::use_module($real_class);
   $class->throw("Module $real_class does not implement a community IO stream")
       unless $real_class->does('Bio::Community::Role::IO');

   $params = $real_class->BUILDARGS(%$params);
   my $self = Class::MOP::Class->initialize($real_class)->new_object($params);

   return $self;
}


method BUILD ($args) {
   # Start IOs
   $self->_initialize_io(%$args);
   return 1;
}


=head2 next_member

 Usage   : my ($member, $count) = $in->next_member;
 Function: Get the next member from the community and its abundance. This
           function is implemented by the Bio::Community::IO::Driver used to
           parse the given file format.
 Args    : None
 Returns : An array containing:
             A Bio::Community::Member object (or undef)
             A positive number (or undef)

=cut

method next_member () {
   $self->throw_not_implemented;
}


=head2 next_community

 Usage   : my $community = $in->next_community;
 Function: Get the next community. Note that communities without members are
           skipped.
 Args    : None
 Returns : A Bio::Community object
             or
           undef if there were no communities left

=cut

method next_community () {
   my $community;

   if (not defined $self->_meta) {
      $self->_next_metacommunity_init( );