fasta_util 0.2.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+  gem "rcov", ">= 0"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    git (1.2.5)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.8.7)
+    rcov (0.9.9)
+    shoulda (2.11.3)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0.0)
+  jeweler (~> 1.5.2)
+  rcov
+  shoulda

data/LICENSE.txt

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+Copyright (c) 2011 robsyme
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= fasta_util
+
+Description goes here.
+
+== Contributing to fasta_util
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2011 robsyme. See LICENSE.txt for
+further details.
+

data/Rakefile

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "fasta_util"
+  gem.homepage = "http://github.com/robsyme/fasta_util"
+  gem.license = "MIT"
+  gem.summary = %Q{A simple tool for performing common tasks with fasta files.}
+  gem.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.}
+  gem.email = "rob.syme@gmail.com"
+  gem.authors = ["robsyme"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  gem.add_runtime_dependency 'bio', '>= 1.4.1'
+  gem.add_runtime_dependency 'thor', '>= 0.14.6'
+  gem.add_development_dependency 'rspec', '>= 1.2.3'
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "fasta_util #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.2.0

data/bin/fasta_util

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+#!/usr/bin/env ruby
+require 'fasta_util'
+
+FastaUtility.start

data/fasta_util.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{fasta_util}
+  s.version = "0.2.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["robsyme"]
+  s.date = %q{2011-02-17}
+  s.default_executable = %q{fasta_util}
+  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.}
+  s.email = %q{rob.syme@gmail.com}
+  s.executables = ["fasta_util"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/fasta_util",
+    "fasta_util.gemspec",
+    "lib/fasta_util.rb",
+    "test/helper.rb",
+    "test/test_fasta_util.rb"
+  ]
+  s.homepage = %q{http://github.com/robsyme/fasta_util}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.5.0}
+  s.summary = %q{A simple tool for performing common tasks with fasta files.}
+  s.test_files = [
+    "test/helper.rb",
+    "test/test_fasta_util.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_runtime_dependency(%q<thor>, [">= 0.14.6"])
+      s.add_development_dependency(%q<rspec>, [">= 1.2.3"])
+    else
+      s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+      s.add_dependency(%q<thor>, [">= 0.14.6"])
+      s.add_dependency(%q<rspec>, [">= 1.2.3"])
+    end
+  else
+    s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+    s.add_dependency(%q<thor>, [">= 0.14.6"])
+    s.add_dependency(%q<rspec>, [">= 1.2.3"])
+  end
+end
+

data/lib/fasta_util.rb

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+require 'thor'
+require 'bio'
+
+class FastaUtility < Thor
+  include Thor::Actions
+  Struct.new("Stats", :sum, :l50, :n50, :count, :mean, :median)
+  
+  no_tasks do
+    def stats(lengths)
+      lengths = lengths.sort{|a, b| b <=> a}
+      stats = Struct::Stats.new
+      
+      temp_sum = 0
+      stats[:sum] = lengths.inject(:+)
+      stats[:l50] = lengths.find{|length| (temp_sum += length) > stats[:sum]/2.0}
+      stats[:n50] = lengths.count{|length| length >= stats[:l50]}
+      stats[:mean] = stats[:sum].to_f/lengths.length
+      stats[:median] = (lengths.length % 2 == 0) ? (lengths[lengths.length/2-1] + lengths[lengths.length/2])/2.0 : lengths[lengths.length/2]
+      stats[:count] = lengths.count
+      return stats
+    end
+    
+    def format(stats)
+      output = []
+      buffer_length = stats.members.map{|key| key.length}.max
+      stats.each_pair do |key, value|
+        numtype = value.is_a?(Float) ? "f" : "d"
+        output << "  %-#{buffer_length}s: %#{numtype}" % [key.to_s.capitalize, value]
+      end
+      output.join("\n")
+    end
+  end
+  
+  desc "filecheck", "Checks to see if a given file exists. Used internally, don't worry about it too much", :hide => true
+  def filecheck(filename)
+    say "The file '#{filename}' doesn't seem to exist!", :red unless File.exists?(filename)
+  end
+  
+  desc "lengths", "Print a set of summary statistics for the given fasta file, including L50, N50, sum and count."
+  method_options [:cutoff, '-c'] => 0
+  def lengths(filename)
+    invoke :filecheck
+    lengths =  Bio::FlatFile.open(filename).map{|entry| (entry.seq[-1,1] == "*") ? entry.length - 1 : entry.length}
+    
+    say "All entries", :green
+    puts format(stats(lengths))
+    if options.cutoff > 0
+      say "Entries with length >= #{options.cutoff}", :green
+      puts format(stats(lengths.find_all{|l| l >= options.cutoff}))
+    end
+  end
+  
+  desc "filter FILENAME [options]", "Impose a filter or set of filters on entries in a fasta file."
+  long_desc "Impose a filter or set of filters on entries in a fasta file where each sequence in the file has to pass all of the filters to be printed."
+  method_option :length_cutoff, :aliases => '-l', :type => :numeric, :default => 0,  :desc => 'Only entries with length >= cutoff will be returned.'
+  method_option :inverse_match,  :aliases => '-v', :type => :boolean, :desc => "Return the inverse of the match after all the other filters have been applied."
+  method_option :defline_grep,  :aliases => '-d', :type => :string,  :default => '', :desc => "A regular expression, used to search the entry's definition line."
+  def filter(filename)
+    invoke :filecheck
+    Bio::FlatFile.open(filename).each do |entry|
+      passed = true
+      passed &&= (entry.length >= options.length_cutoff)
+      passed &&= (entry.definition.match(Regexp.new(options.defline_grep)))
+      passed = !passed if options.inverse_match
+      puts entry if passed
+    end
+  end
+  
+  desc "clean FILENAME [options]", "Clean up a fasta file"
+  method_option :wrap_width, :aliases => '-w', :type => :numeric, :desc => 'Wrap the fasta to N columns'
+  def clean(filename)
+    invoke :filecheck
+    Bio::FlatFile.open(filename).each do |entry|
+      puts entry.to_biosequence.output(:fasta, :header => entry.definition, :width => options.wrap_width)
+    end
+  end
+  
+  
+  desc "sort FILENAME [options]", "Sorts a fasta file according to criteria"
+  def sort(filename)
+    invoke :filecheck
+    Bio::FlatFile.open(filename).to_a.sort{|a,b| b.length <=> a.length}.each do |entry|
+      puts entry
+    end
+  end
+end

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'fasta_util'
+
+class Test::Unit::TestCase
+end

data/test/test_fasta_util.rb

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+require 'helper'
+
+class TestFastaUtil < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: fasta_util
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.2.0
+platform: ruby
+authors: 
+- robsyme
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-02-17 00:00:00 +08:00
+default_executable: fasta_util
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: shoulda
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.4.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: thor
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.14.6
+  type: :runtime
+  prerelease: false
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.2.3
+  type: :development
+  prerelease: false
+  version_requirements: *id007
+description: Easy fasta filtering, wrapping, calculating common statistics, sorting etc. Based on the fasta_tool script that I think was written by Jason Stajich.
+email: rob.syme@gmail.com
+executables: 
+- fasta_util
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.rdoc
+files: 
+- .document
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/fasta_util
+- fasta_util.gemspec
+- lib/fasta_util.rb
+- test/helper.rb
+- test/test_fasta_util.rb
+has_rdoc: true
+homepage: http://github.com/robsyme/fasta_util
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -4274301518574144620
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.5.0
+signing_key: 
+specification_version: 3
+summary: A simple tool for performing common tasks with fasta files.
+test_files: 
+- test/helper.rb
+- test/test_fasta_util.rb