Bio-Community
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lib/Bio/Community.pm view on Meta::CPAN
=cut
package Bio::Community;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Member;
our $VERSION = '0.001008'; # 0.1.8
extends 'Bio::Root::Root';
=head2 name
Function: Get or set the name of the community
lib/Bio/Community/Alpha.pm view on Meta::CPAN
=cut
package Bio::Community::Alpha;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use List::Util qw(max);
extends 'Bio::Root::Root';
=head2 community
Function: Get or set the community to process.
Usage : my $community = $alpha->community();
Args : A Bio::Community object
lib/Bio/Community/IO.pm view on Meta::CPAN
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',
lib/Bio/Community/IO/Driver/biom.pm view on Meta::CPAN
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::IO::Driver::biom;
use Moose;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Member;
use Bio::Community::TaxonomyUtils;
use JSON::XS qw( decode_json encode_json );
use DateTime;
use constant BIOM_NAME => 'Biological Observation Matrix 1.0';
use constant BIOM_URL => 'http://biom-format.org/documentation/format_versions/biom-1.0.html';
use constant BIOM_MATRIX_TYPE => 'sparse'; # sparse or dense
use constant BIOM_TYPE => 'OTU table';
# "XYZ table" where XYZ is Pathway, Gene, Function, Ortholog, Metabolite or Taxon
lib/Bio/Community/IO/Driver/dummy.pm view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::IO::Driver::dummy;
use Moose;
use namespace::autoclean;
use Method::Signatures;
extends 'Bio::Community::IO';
with 'Bio::Community::Role::IO';
our $multiple_communities = 0; # the format supports one community per file
our $default_sort_members = 0; # members not sorted by abundance
our $default_abundance = 'count'; # report raw counts
our $default_missing_string = '-'; # empty members represented as '-'
lib/Bio/Community/IO/Driver/gaas.pm view on Meta::CPAN
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::IO::Driver::gaas;
use Moose;
use namespace::autoclean;
use Method::Signatures;
use Bio::Community::Member;
extends 'Bio::Community::IO';
with 'Bio::Community::Role::IO';
our $multiple_communities = 0; # the format supports one community per file
our $explicit_ids = 1; # IDs are explicitly recorded
our $default_sort_members = -1; # sorted by decreasing abundance
lib/Bio/Community/IO/Driver/generic.pm view on Meta::CPAN
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::IO::Driver::generic;
use Moose;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Member;
extends 'Bio::Community::IO';
with 'Bio::Community::Role::IO',
'Bio::Community::Role::Table';
our $multiple_communities = 1; # format supports several communities per file
our $explicit_ids = 0; # IDs are not explicitly recorded
#### sorting only effective for first community???
lib/Bio/Community/IO/Driver/qiime.pm view on Meta::CPAN
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::IO::Driver::qiime;
use Moose;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Member;
extends 'Bio::Community::IO';
with 'Bio::Community::Role::IO',
'Bio::Community::Role::Table';
our $multiple_communities = 1; # format supports several communities per file
our $explicit_ids = 1; # IDs are explicitly recorded
#### sorting only effective for first community???
lib/Bio/Community/IO/Driver/unifrac.pm view on Meta::CPAN
it under the same terms as Perl itself, either Perl version 5.10.1 or,
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::IO::Driver::unifrac;
use Moose;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Member;
extends 'Bio::Community::IO';
with 'Bio::Community::Role::IO',
'Bio::Community::Role::Table';
our $multiple_communities = 1; # format supports several communities per file
our $explicit_ids = 0; # IDs are not explicitly recorded
#### sorting only effective for first community???
lib/Bio/Community/IO/FormatGuesser.pm view on Meta::CPAN
=cut
package Bio::Community::IO::FormatGuesser;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
extends 'Bio::Root::Root';
my %formats = (
biom => \&_possibly_biom ,
gaas => \&_possibly_gaas ,
unifrac => \&_possibly_unifrac ,
generic => \&_possibly_generic ,
qiime => \&_possibly_qiime ,
lib/Bio/Community/Member.pm view on Meta::CPAN
Returns : a new Bio::Community::Member object
=cut
package Bio::Community::Member;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use namespace::autoclean;
use Method::Signatures;
use Bio::Community::Types;
extends 'Bio::Root::Root';
with 'Bio::Community::Role::Described' , # -desc
'Bio::Community::Role::Classified', # -taxon
'Bio::Community::Role::Sequenced' , # -seqs
'Bio::Community::Role::Weighted' ; # -weights
lib/Bio/Community/Meta.pm view on Meta::CPAN
=cut
package Bio::Community::Meta;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use Tie::IxHash;
use Bio::Community;
use Bio::Community::Member;
extends 'Bio::Root::Root';
method BUILD ($args) {
# Process -communities constructor
lib/Bio/Community/Meta/Beta.pm view on Meta::CPAN
=cut
package Bio::Community::Meta::Beta;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use List::Util qw(min max);
use Bio::Community::Meta;
extends 'Bio::Root::Root';
=head2 metacommunity
Function: Get or set the communities to process, given as a metacommunity.
Usage : my $meta = $beta->metacommunity;
lib/Bio/Community/Meta/Gamma.pm view on Meta::CPAN
=cut
package Bio::Community::Meta::Gamma;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use List::Util qw(max);
use Bio::Community::Alpha;
extends 'Bio::Root::Root';
=head2 metacommunity
Function: Get or set the communities to process, given as a metacommunity.
Usage : my $meta = $gamma->metacommunity;
lib/Bio/Community/Role/Classified.pm view on Meta::CPAN
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::Classified;
use Moose::Role;
use namespace::autoclean;
=head2 taxon
Usage : my $taxon = $member->taxon();
Function: Get or set a taxon (or species) for this object.
Args : A Bio::Taxon object
Returns : A Bio::Taxon object
=cut
lib/Bio/Community/Role/Described.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::Described;
use Moose::Role;
use namespace::autoclean;
=head2 desc
Usage : my $description = $member->desc();
Function: Get or set a description for this object.
Args : A string
Returns : A string
=cut
lib/Bio/Community/Role/IO.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::IO;
use Moose::Role;
use namespace::autoclean;
# TODO: POD that describes each method and its inputs and outputs
requires
# Methods implemented by the Bio::Community::IO::* drivers
'_next_community_init',
'_next_community_finish',
'_write_community_init',
'_write_community_finish',
'_next_metacommunity_init',
lib/Bio/Community/Role/Locked.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::Locked;
use Moose::Role;
use Method::Signatures;
use namespace::autoclean;
use Hash::Util ();
=head2 lock
Usage : $member->lock();
Function: Lock the object, making it read-only.
Args : None
Returns : 1 for success
lib/Bio/Community/Role/PRNG.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::PRNG;
use Moose::Role;
use namespace::autoclean;
use Method::Signatures;
use Bio::Community::Types;
has _prng => (
is => 'rw',
#isa => 'Math::GSL::RNG',
default => sub {
if (not eval { require Math::GSL::RNG }) {
shift->throw("Need module require Math::GSL::RNG for PRNG role\n$@");
lib/Bio/Community/Role/Sequenced.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::Sequenced;
use Moose::Role;
use namespace::autoclean;
=head2 seqs
Usage : my $seqs = $member->seqs();
Function: Get or set some sequences for this object.
Args : An arrayref of Bio::SeqI objects
Returns : An arrayref of Bio::SeqI objects
=cut
lib/Bio/Community/Role/Table.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::Table;
use Moose::Role;
use Method::Signatures;
use namespace::autoclean;
use Fcntl;
# Consuming class has to inherit from Bio::Root::IO
requires '_fh',
'_readline',
'_print';
=head2 delim
lib/Bio/Community/Role/Weighted.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Community::Role::Weighted;
use Moose::Role;
use namespace::autoclean;
use Method::Signatures;
use Bio::Community::Types;
=head2 weights
Usage : my $weights = $member->weights();
Function: Get or set some weights for this object. Weights represent how biased
the sampling of this organism is. For example, when random shotgun
sequencing microorganisms in the environment, the relative abundance
lib/Bio/Community/Tools/Accumulator.pm view on Meta::CPAN
Returns : a new Bio::Community::Tools::Accumulator object
=cut
package Bio::Community::Tools::Accumulator;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use namespace::autoclean;
use Bio::Community::Alpha;
use Bio::Community::Meta;
use Bio::Community::Tools::Rarefier;
use List::Util qw( shuffle );
use Method::Signatures;
extends 'Bio::Root::Root';
=head2 metacommunity
lib/Bio/Community/Tools/IdConverter.pm view on Meta::CPAN
=cut
package Bio::Community::Tools::IdConverter;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::IO;
use Bio::Community::Meta;
extends 'Bio::Root::Root';
=head2 metacommunity
Function: Get/set communities, given as metacommunity, to summarize.
lib/Bio/Community/Tools/Rarefier.pm view on Meta::CPAN
Returns : a new Bio::Community::Tools::Rarefier object
=cut
package Bio::Community::Tools::Rarefier;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use namespace::autoclean;
use Bio::Community::Meta;
use Bio::Community::Meta::Beta;
use List::Util qw(min);
use Method::Signatures;
use POSIX; # defines DBL_EPSILON to something like 2.22044604925031e-16
use constant REL_EPSILON => 1 + 10 * DBL_EPSILON;
extends 'Bio::Root::Root';
with 'Bio::Community::Role::PRNG';
lib/Bio/Community/Tools/Sampler.pm view on Meta::CPAN
=cut
package Bio::Community::Tools::Sampler;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use List::Util qw(first);
use namespace::autoclean;
use Bio::Community;
extends 'Bio::Root::Root';
with 'Bio::Community::Role::PRNG';
=head2 community
Function: Get or set the community to sample from.
Usage : my $community = $sampler->community();
lib/Bio/Community/Tools/ShrapnelCleaner.pm view on Meta::CPAN
=cut
package Bio::Community::Tools::ShrapnelCleaner;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
extends 'Bio::Root::Root';
=head2 metacommunity
Function: Get or set the communities to process.
Usage : my $communities = $cleaner->communities;
Args : A Bio::Community::Meta object
Returns : A Bio::Community::Meta object
lib/Bio/Community/Tools/Summarizer.pm view on Meta::CPAN
=cut
package Bio::Community::Tools::Summarizer;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::IO;
use Bio::Community::Meta;
use Bio::Community::TaxonomyUtils
qw(get_taxon_lineage get_lineage_string clean_lineage_arr);
use POSIX; # defines DBL_EPSILON to something like 2.22044604925031e-16
use constant EPSILON => 100 * DBL_EPSILON; # suggested in "Mastering Algorithms in Perl"
extends 'Bio::Root::Root';
lib/Bio/Community/Tools/Transformer.pm view on Meta::CPAN
=cut
package Bio::Community::Tools::Transformer;
use Moose;
use MooseX::NonMoose;
use MooseX::StrictConstructor;
use Method::Signatures;
use namespace::autoclean;
use Bio::Community::Meta;
use Scalar::Util;
extends 'Bio::Root::Root';
=head2 metacommunity
Function: Get or set the metacommunity to normalize.
lib/Bio/Community/Types.pm view on Meta::CPAN
at your option, any later version of Perl 5 you may have available.
=cut
package Bio::Community::Types;
use Moose;
use Moose::Util::TypeConstraints;
use Method::Signatures;
use namespace::autoclean;
# Numbers
subtype 'PositiveNum'
=> as 'Num'
=> where { $_ >= 0 }
=> message { _gen_err_msg('a positive number', $_) };
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