Bio-MUST-Core

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META.yml  view on Meta::CPAN

  POSIX: '0'
  Path::Class: '0'
  Regexp::Common: '0'
  Scalar::Util: '0'
  Smart::Comments: '0'
  Statistics::Descriptive: '0'
  Storable: '0'
  Test::Files: '0'
  Test::Most: '0'
  Tie::IxHash: '0'
  Try::Tiny: '0'
  Try::Tiny::Warnings: '0'
  XML::Bare: '0.53'
  YAML::XS: '0'
  aliased: '0'
  autodie: '0'
  feature: '0'
  namespace::autoclean: '0'
  perl: '5.013002'
  strict: '0'
  warnings: '0'
version: '0.251810'

Makefile.PL  view on Meta::CPAN

    "POSIX" => 0,
    "Path::Class" => 0,
    "Regexp::Common" => 0,
    "Scalar::Util" => 0,
    "Smart::Comments" => 0,
    "Statistics::Descriptive" => 0,
    "Storable" => 0,
    "Test::Files" => 0,
    "Test::Most" => 0,
    "Tie::IxHash" => 0,
    "Try::Tiny" => 0,
    "Try::Tiny::Warnings" => 0,
    "XML::Bare" => "0.53",
    "YAML::XS" => 0,
    "aliased" => 0,
    "autodie" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0,
    "strict" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {

Makefile.PL  view on Meta::CPAN

  "Path::Class" => 0,
  "Regexp::Common" => 0,
  "Scalar::Util" => 0,
  "Smart::Comments" => 0,
  "Statistics::Descriptive" => 0,
  "Storable" => 0,
  "Test::Deep" => 0,
  "Test::Files" => 0,
  "Test::Most" => 0,
  "Tie::IxHash" => 0,
  "Try::Tiny" => 0,
  "Try::Tiny::Warnings" => 0,
  "XML::Bare" => "0.53",
  "YAML::XS" => 0,
  "aliased" => 0,
  "autodie" => 0,
  "feature" => 0,
  "namespace::autoclean" => 0,
  "strict" => 0,
  "warnings" => 0
);

bin/format-tree.pl  view on Meta::CPAN

# PODNAME: format-tree.pl
# ABSTRACT: Format (and annotate) trees for printing
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@uliege.be>

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use List::AllUtils qw(pairfirst);
use Smart::Comments;
use Try::Tiny;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(:filenames secure_outfile);
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::IdMapper';
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Core::Taxonomy';
use aliased 'Bio::MUST::Core::Tree';

# TODO: implement numbered taxonomic levels as in fetch-tax.pl

bin/prune-tree.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: prune-tree.pl
# ABSTRACT: Prune tips from TREE files based on id lists

use Modern::Perl '2011';
use autodie;

use File::Basename;
use Getopt::Euclid qw(:vars);
use Smart::Comments;
use Try::Tiny;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix insert_suffix secure_outfile);
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::Tree';


my $method = $ARGV_from_must ? 'load_lis' : 'load';

IDL:

lib/Bio/MUST/Core/GeneticCode/Factory.pm  view on Meta::CPAN

use autodie;
use feature qw(say);

use Carp;
use Const::Fast;
use File::Spec;
use List::AllUtils qw(uniq);
use LWP::Simple qw(get);
use Path::Class qw(file);
use Try::Tiny;

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::GeneticCode';


# public path to NCBI Taxonomy dump directory
has 'tax_dir' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Types::Dir',
    coerce   => 1,

lib/Bio/MUST/Core/Taxonomy.pm  view on Meta::CPAN

use Const::Fast;
use File::Basename;
use File::Find::Rule;
use IPC::System::Simple qw(system);
use List::AllUtils 0.12
    qw(first firstidx uniq each_array mesh count_by max_by);
use LWP::Simple qw(get getstore);
use Path::Class qw(dir file);
use POSIX;
use Scalar::Util qw(looks_like_number);
use Try::Tiny;
use Try::Tiny::Warnings;
use XML::Bare;

use Bio::LITE::Taxonomy::NCBI::Gi2taxid qw(new_dict);
use Bio::Phylo::IO qw(parse);

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:ncbi :files);
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Core::IdList';