lederhosen 0.3.3 → 0.3.4

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Files changed (4) hide show
  1. data/lederhosen.gemspec +2 -1
  2. data/lib/lederhosen/tasks/split_fasta.rb +33 -0
  3. data/lib/lederhosen/version.rb +1 -1
  4. metadata +106 -101
data/lederhosen.gemspec CHANGED
@@ -5,7 +5,7 @@
5
5
 
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  Gem::Specification.new do |s|
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  s.name = "lederhosen"
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- s.version = "0.3.3"
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+ s.version = "0.3.4"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Austin G. Davis-Richardson"]
@@ -40,6 +40,7 @@ Gem::Specification.new do |s|
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  "lib/lederhosen/tasks/rep_reads.rb",
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  "lib/lederhosen/tasks/sort.rb",
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  "lib/lederhosen/tasks/split.rb",
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+ "lib/lederhosen/tasks/split_fasta.rb",
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  "lib/lederhosen/tasks/squish.rb",
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  "lib/lederhosen/tasks/trim.rb",
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  "lib/lederhosen/tasks/uc_filter.rb",
data/lib/lederhosen/tasks/split_fasta.rb ADDED
@@ -0,0 +1,33 @@
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+ ##
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+ # Split a fasta file into many fasta files with n reads
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+ #
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+
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+ module Lederhosen
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+ class CLI
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+
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+ desc 'split_fasta',
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+ 'splits input fasta file into separate fasta files containing n reads'
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+
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+ method_option :input, :type => :string, :required => true
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+ method_option :out_dir, :type => :string, :required => true
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+ method_option :n, :type => :numeric, :required => true
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+
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+ def split_fasta
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+ input = options[:input]
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+ out_dir = options[:out_dir]
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+ n = options[:n].to_i
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+
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+ ohai "splitting #{input} into files with #{n} reads stored in #{out_dir}"
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+
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+ `mkdir -p #{out_dir}`
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+
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+ File.open input do |handle|
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+ Dna.new(handle).each_with_index do |record, i|
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+ @out = File.open(File.join(out_dir, "split_#{i/n}.fasta"), 'w') if i%n == 0
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+ @out.puts record
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+ end
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+ end
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+
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+ end
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+ end
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+ end
data/lib/lederhosen/version.rb CHANGED
@@ -2,7 +2,7 @@ module Lederhosen
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  module Version
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  MAJOR = 0
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  MINOR = 3
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- PATCH = 3
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+ PATCH = 4
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  STRING = [MAJOR, MINOR, PATCH].join('.')
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  end
metadata CHANGED
@@ -1,120 +1,118 @@
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- --- !ruby/object:Gem::Specification
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+ --- !ruby/object:Gem::Specification
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  name: lederhosen
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- version: !ruby/object:Gem::Version
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- version: 0.3.3
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+ version: !ruby/object:Gem::Version
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+ hash: 27
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  prerelease:
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+ segments:
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+ - 0
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+ - 3
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+ - 4
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+ version: 0.3.4
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  platform: ruby
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- authors:
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+ authors:
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  - Austin G. Davis-Richardson
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-08-14 00:00:00.000000000 Z
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- dependencies:
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- - !ruby/object:Gem::Dependency
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- name: dna
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- requirement: !ruby/object:Gem::Requirement
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+
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+ date: 2012-08-14 00:00:00 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ type: :runtime
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+ requirement: &id001 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - '='
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- - !ruby/object:Gem::Version
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+ requirements:
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+ - - "="
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+ - !ruby/object:Gem::Version
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+ hash: 7
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+ segments:
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+ - 0
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+ - 0
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+ - 12
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  version: 0.0.12
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- type: :runtime
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+ version_requirements: *id001
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+ name: dna
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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+ - !ruby/object:Gem::Dependency
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+ type: :runtime
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+ requirement: &id002 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - '='
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- - !ruby/object:Gem::Version
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- version: 0.0.12
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- - !ruby/object:Gem::Dependency
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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+ version_requirements: *id002
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  name: progressbar
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- requirement: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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+ - !ruby/object:Gem::Dependency
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+ type: :runtime
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+ requirement: &id003 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- - !ruby/object:Gem::Dependency
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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+ version_requirements: *id003
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  name: thor
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- requirement: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- type: :runtime
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- - !ruby/object:Gem::Dependency
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- name: rdoc
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- requirement: !ruby/object:Gem::Requirement
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+ - !ruby/object:Gem::Dependency
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+ type: :development
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+ requirement: &id004 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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+ requirements:
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  - - ~>
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- - !ruby/object:Gem::Version
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- version: '3.12'
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- type: :development
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+ - !ruby/object:Gem::Version
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+ hash: 31
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+ segments:
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+ - 3
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+ - 12
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+ version: "3.12"
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+ version_requirements: *id004
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+ name: rdoc
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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+ - !ruby/object:Gem::Dependency
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+ type: :development
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+ requirement: &id005 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ~>
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- - !ruby/object:Gem::Version
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- version: '3.12'
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- - !ruby/object:Gem::Dependency
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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+ version_requirements: *id005
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  name: bundler
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- requirement: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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+ - !ruby/object:Gem::Dependency
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+ type: :development
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+ requirement: &id006 !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- - !ruby/object:Gem::Dependency
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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+ version_requirements: *id006
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  name: jeweler
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- requirement: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- type: :development
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  prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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  description: Various tools for OTU clustering
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  email: harekrishna@gmail.com
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- executables:
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+ executables:
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  - lederhosen
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  extensions: []
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- extra_rdoc_files:
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+
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+ extra_rdoc_files:
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  - LICENSE.txt
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- files:
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+ files:
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  - .rspec
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  - .rvmrc
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  - Gemfile
@@ -138,6 +136,7 @@ files:
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  - lib/lederhosen/tasks/rep_reads.rb
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  - lib/lederhosen/tasks/sort.rb
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  - lib/lederhosen/tasks/split.rb
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+ - lib/lederhosen/tasks/split_fasta.rb
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  - lib/lederhosen/tasks/squish.rb
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  - lib/lederhosen/tasks/trim.rb
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  - lib/lederhosen/tasks/uc_filter.rb
@@ -157,31 +156,37 @@ files:
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  - spec/misc_spec.rb
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  - spec/spec_helper.rb
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  homepage: http://audy.github.com/lederhosen
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- licenses:
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+ licenses:
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  - MIT
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  post_install_message:
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  rdoc_options: []
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- require_paths:
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+
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+ require_paths:
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  - lib
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- required_ruby_version: !ruby/object:Gem::Requirement
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+ required_ruby_version: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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- segments:
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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  - 0
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- hash: 1714359518753916587
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- required_rubygems_version: !ruby/object:Gem::Requirement
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+ version: "0"
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ! '>='
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- - !ruby/object:Gem::Version
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- version: '0'
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ hash: 3
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+ segments:
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+ - 0
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+ version: "0"
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  requirements: []
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+
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  rubyforge_project:
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  rubygems_version: 1.8.24
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  signing_key:
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  specification_version: 3
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  summary: OTU Clustering
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  test_files: []
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+