Bio-FastParsers

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META.yml  view on Meta::CPAN

  Exporter::Easy: '0'
  List::AllUtils: '0'
  Moose: '0'
  Moose::Role: '0'
  Moose::Util::TypeConstraints: '0'
  Path::Class: '0'
  Smart::Comments: '0'
  Sort::Naturally: '0'
  Test::Most: '0'
  Tie::IxHash: '0'
  Try::Tiny: '0'
  XML::Bare: '0.53'
  aliased: '0'
  autodie: '0'
  feature: '0'
  namespace::autoclean: '0'
  perl: v5.10.0
  strict: '0'
  warnings: '0'
version: '0.221230'
x_generated_by_perl: v5.26.3

Makefile.PL  view on Meta::CPAN

    "Exporter::Easy" => 0,
    "List::AllUtils" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Moose::Util::TypeConstraints" => 0,
    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Sort::Naturally" => 0,
    "Test::Most" => 0,
    "Tie::IxHash" => 0,
    "Try::Tiny" => 0,
    "XML::Bare" => "0.53",
    "aliased" => 0,
    "autodie" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0,
    "strict" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {
    "Test::Most" => 0

Makefile.PL  view on Meta::CPAN

  "Exporter::Easy" => 0,
  "List::AllUtils" => 0,
  "Moose" => 0,
  "Moose::Role" => 0,
  "Moose::Util::TypeConstraints" => 0,
  "Path::Class" => 0,
  "Smart::Comments" => 0,
  "Sort::Naturally" => 0,
  "Test::Most" => 0,
  "Tie::IxHash" => 0,
  "Try::Tiny" => 0,
  "XML::Bare" => "0.53",
  "aliased" => 0,
  "autodie" => 0,
  "feature" => 0,
  "namespace::autoclean" => 0,
  "strict" => 0,
  "warnings" => 0
);

lib/Bio/FastParsers/Roles/Clusterable.pm  view on Meta::CPAN

# ABSTRACT: Attributes and methods common to CD-HIT and UCLUST drivers
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
$Bio::FastParsers::Roles::Clusterable::VERSION = '0.221230';
use Moose::Role;

use autodie;
use feature qw(say);

use Carp;
use Sort::Naturally;
use Try::Tiny;


# private attributes

has '_members_for' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[ArrayRef[Str]]',
    init_arg => undef,
    writer   => '_set_members_for',

t/clusterable.t  view on Meta::CPAN

#!/usr/bin/env perl

use Test::Most;

use autodie;
use feature qw(say);

use Path::Class qw(file);
use Tie::IxHash;
use Try::Tiny;

use Bio::FastParsers;


# perl -nle 'if (m/Cluster (\d+)/) { $cluster = $1; next } ($id,$type) = m/>(\S+)\.{3} (\*|at)/; $hash{$cluster}{repr} = $id if $type eq q{*}; push @{$hash{$cluster}{memb}}, $id if $type eq q{at}; END{ for $cluster (sort { $a <=> $b } keys %hash) { p...

# perl -MSort::Naturally -nle 'my ($id, $member_str) = split ": "; my @members = split q{ }, $member_str; $hash{$id} = \@members; END{ @list = sort { scalar @{$hash{$b}} <=> scalar @{$hash{$a}} || ncmp($a, $b) } keys %hash; print join "\n", @list }' ...

# for f in `cat cdHit.out.ids`; do grep $f cdHit.out.groups ; done