bio-gadget 0.1.0

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*~
+.#*
+.fuse*
+

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bio-gadget.gemspec
+gemspec

data/Gthorfile

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+module Bio
+  class Gadget < Thor
+
+    namespace :bio
+
+    desc 'qvstat QUAL', 'statistics of quality values in *.qual file'
+    def qvstat(qualfile)
+      stat = Hash.new
+      myopen(qualfile) { |fp|
+        fp.each { |line|
+          next if /^[\#\>]/ =~ line
+          qvs = line.rstrip.split
+          qvs.each_index { |i|
+            qv = qvs[i]
+            stat[qv] = Array.new unless stat.key?(qv)
+            if stat[qv][i].nil?
+              stat[qv][i] = 1
+            else
+              stat[qv][i] += 1
+            end
+          }
+        }
+      }
+      statfile = qualfile.sub(/.qual(.gz)?$/, '.qvstat')
+      open(statfile, 'w') { |out|
+        qvs = stat.keys.sort { |a, b| a.to_i <=> b.to_i }
+        qvs.each { |qv|
+          out.puts "#{qv} #{stat[qv].join(' ')}"
+        }
+      }
+    end
+
+    private
+
+    def myopen(file, &block)
+      # how to write?
+      f = (/\|/ !~ file && /\.gz$/ =~ file) ? "| gunzip -c #{file}" : file
+      unless block.nil?
+        o = open(f); block.call(o); o.close
+      else
+        open(f)
+      end
+    end
+
+  end
+end

data/LICENSE

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+Copyright (c) 2012 Shintaro Katayama
+
+MIT License
+
+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.org

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+* Bio::Gadget
+
+*Bio::Gadget* - Gadgets for bioinformatics
+
+* Installation
+
+: gem install bio-gadget
+
+* Usage
+
+: gthor help bio
+: gthor list bio
+
+* Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Added some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+#!/usr/bin/env rake
+require "bundler/gem_tasks"

data/bio-gadget.gemspec

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+# -*- encoding: utf-8 -*-
+require File.expand_path('../lib/bio-gadget/version', __FILE__)
+
+Gem::Specification.new do |gem|
+  gem.authors       = ["Shintaro Katayama"]
+  gem.email         = ["shintaro.katayama@gmail.com"]
+  gem.description   = %q{Gadgets for bioinformatics}
+  gem.summary       = gem.description
+  gem.homepage      = "https://github.com/shka/ruby-bio-gadget"
+
+  gem.files         = `git ls-files`.split($\)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.name          = "bio-gadget"
+  gem.require_paths = ["lib"]
+  gem.version       = Bio::Gadget::VERSION
+
+  gem.add_dependency 'gthor'
+end

data/lib/bio-gadget.rb

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+require "bio-gadget/version"
+
+module Bio
+  module Gadget
+    # Your code goes here...
+  end
+end

data/lib/bio-gadget/version.rb

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+module Bio
+  module Gadget
+    VERSION = "0.1.0"
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-gadget
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Shintaro Katayama
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-08-20 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: gthor
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Gadgets for bioinformatics
+email:
+- shintaro.katayama@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- Gthorfile
+- LICENSE
+- README.org
+- Rakefile
+- bio-gadget.gemspec
+- lib/bio-gadget.rb
+- lib/bio-gadget/version.rb
+homepage: https://github.com/shka/ruby-bio-gadget
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.23
+signing_key: 
+specification_version: 3
+summary: Gadgets for bioinformatics
+test_files: []