fasta_util 0.5.1 → 0.5.2

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Files changed (4) hide show
  1. data/VERSION +1 -1
  2. data/bin/fasta_util +3 -0
  3. data/fasta_util.gemspec +8 -9
  4. metadata +69 -74
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.5.1
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+ 0.5.2
data/bin/fasta_util CHANGED
@@ -60,15 +60,18 @@ class FastaUtility < Thor
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  method_option :inverse_match, :aliases => '-v', :type => :boolean, :desc => "Return the inverse of the match after all the other filters have been applied."
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  method_option :defline_grep, :aliases => '-d', :type => :string, :default => '', :desc => "A regular expression, used to search the entry's definition line."
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  method_option :definitions_file, :aliases => '-f', :type => :string, :default => '', :desc => "A file with definitions to match, one per line."
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+ method_option :entry_id_file, :aliases => '-e', :type => :string, :default => '', :desc => "A file with entry_ids to match, one per line."
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  def filter(filename)
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  invoke :filecheck
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  invoke :filecheck, [options.definitions_file]
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  requested_definitions = File.open(options.definitions_file).map{|definition| definition.strip} unless options.definitions_file == ''
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+ entry_ids = File.open(options.entry_id_file).map{|id| id.strip} unless options.entry_id_file == ''
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  Bio::FlatFile.open(filename).each do |entry|
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  passed = true
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  passed &&= (entry.length >= options.length_cutoff)
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  passed &&= (entry.definition.match(Regexp.new(options.defline_grep)))
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  passed &&= (requested_definitions.include? entry.definition) unless options.definitions_file == ''
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+ passed &&= (entry_ids.include? entry.entry_id) unless options.entry_id_file == ''
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  passed = !passed if options.inverse_match
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  puts entry if passed
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  end
data/fasta_util.gemspec CHANGED
@@ -4,15 +4,14 @@
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  # -*- encoding: utf-8 -*-
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  Gem::Specification.new do |s|
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- s.name = %q{fasta_util}
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- s.version = "0.5.1"
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+ s.name = "fasta_util"
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+ s.version = "0.5.2"
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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 = ["robsyme"]
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- s.date = %q{2011-07-13}
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- s.default_executable = %q{fasta_util}
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- s.description = %q{Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.}
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- s.email = %q{rob.syme@gmail.com}
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+ s.date = "2011-11-18"
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+ s.description = "Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich."
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+ s.email = "rob.syme@gmail.com"
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  s.executables = ["fasta_util"]
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  s.extra_rdoc_files = [
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  "LICENSE.txt",
@@ -31,11 +30,11 @@ Gem::Specification.new do |s|
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  "test/helper.rb",
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  "test/test_fasta_util.rb"
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  ]
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- s.homepage = %q{http://github.com/robsyme/fasta_util}
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+ s.homepage = "http://github.com/robsyme/fasta_util"
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  s.licenses = ["MIT"]
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  s.require_paths = ["lib"]
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- s.rubygems_version = %q{1.5.0}
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- s.summary = %q{A simple tool for performing common tasks with fasta files.}
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+ s.rubygems_version = "1.8.10"
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+ s.summary = "A simple tool for performing common tasks with fasta files."
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  s.test_files = [
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  "test/helper.rb",
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  "test/test_fasta_util.rb"
metadata CHANGED
@@ -1,105 +1,103 @@
1
- --- !ruby/object:Gem::Specification
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+ --- !ruby/object:Gem::Specification
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  name: fasta_util
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- version: !ruby/object:Gem::Version
3
+ version: !ruby/object:Gem::Version
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+ version: 0.5.2
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  prerelease:
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- version: 0.5.1
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  platform: ruby
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- authors:
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+ authors:
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  - robsyme
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  autorequire:
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  bindir: bin
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  cert_chain: []
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-
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- date: 2011-07-13 00:00:00 +08:00
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- default_executable: fasta_util
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- dependencies:
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- - !ruby/object:Gem::Dependency
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+ date: 2011-11-18 00:00:00.000000000Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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  name: shoulda
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- requirement: &id001 !ruby/object:Gem::Requirement
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+ requirement: &19773680 !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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+ version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *19773680
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+ - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &id002 !ruby/object:Gem::Requirement
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+ requirement: &19706300 !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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+ - !ruby/object:Gem::Version
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *id002
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *19706300
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+ - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &id003 !ruby/object:Gem::Requirement
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+ requirement: &19705760 !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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+ - !ruby/object:Gem::Version
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  version: 1.5.2
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  type: :development
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  prerelease: false
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- version_requirements: *id003
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *19705760
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+ - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &id004 !ruby/object:Gem::Requirement
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+ requirement: &19705160 !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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+ version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *id004
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *19705160
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+ - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &id005 !ruby/object:Gem::Requirement
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+ requirement: &19704640 !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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  version: 1.4.1
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  type: :runtime
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  prerelease: false
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- version_requirements: *id005
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *19704640
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+ - !ruby/object:Gem::Dependency
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  name: thor
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- requirement: &id006 !ruby/object:Gem::Requirement
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+ requirement: &19704080 !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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  version: 0.14.6
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  type: :runtime
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  prerelease: false
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- version_requirements: *id006
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- - !ruby/object:Gem::Dependency
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+ version_requirements: *19704080
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+ - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &id007 !ruby/object:Gem::Requirement
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+ requirement: &19703600 !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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  version: 1.2.3
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  type: :development
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  prerelease: false
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- version_requirements: *id007
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- description: Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.
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+ version_requirements: *19703600
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+ description: Easy fasta filtering, wrapping, calculating common statistics, sorting
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+ etc. Based on the fasta_tool script that I think was written by Jason Stajich.
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  email: rob.syme@gmail.com
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- executables:
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+ executables:
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  - fasta_util
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  extensions: []
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-
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- extra_rdoc_files:
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+ extra_rdoc_files:
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  - LICENSE.txt
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  - README.rdoc
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- files:
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+ files:
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  - .document
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  - Gemfile
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  - Gemfile.lock
@@ -111,37 +109,34 @@ files:
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  - fasta_util.gemspec
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  - test/helper.rb
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  - test/test_fasta_util.rb
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- has_rdoc: true
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  homepage: http://github.com/robsyme/fasta_util
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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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-
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- require_paths:
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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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- hash: 107780182399010435
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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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+ version: '0'
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+ segments:
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  - 0
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- version: "0"
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- required_rubygems_version: !ruby/object:Gem::Requirement
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+ hash: -1315820014973782293
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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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+ version: '0'
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  requirements: []
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-
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  rubyforge_project:
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- rubygems_version: 1.5.0
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+ rubygems_version: 1.8.10
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  signing_key:
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  specification_version: 3
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  summary: A simple tool for performing common tasks with fasta files.
145
- test_files:
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+ test_files:
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  - test/helper.rb
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  - test/test_fasta_util.rb