qu-utils 1.0.1

checksums.yaml

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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
+test

data/Gemfile

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

data/LICENSE.txt

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+Copyright (c) 2013 Wubin Qu
+
+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.md

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+# Qu::Utils
+
+Utils: useful class or methods used in qu-* projects.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'qu-utils'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install qu-utils
+
+## Usage
+
+```
+require 'qu/utils'
+
+Qu::Utils::long_seq_wrap(long_seq)
+```
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"

data/lib/qu/utils.rb

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+require 'bio'
+require 'optparse'
+require "qu/utils/version"
+
+module Qu
+  module Utils
+    IUPAC = {
+      A: ['A'],
+      T: ['T'],
+      C: ['C'],
+      G: ['G'],
+      R: ['G', 'A'],
+      Y: ['T', 'C'],
+      S: ['G', 'C'],
+      W: ['T', 'A'],
+      K: ['G', 'T'],
+      M: ['A', 'C'],
+      D: ['G', 'T', 'A'],
+      H: ['T', 'A', 'C'],
+      B: ['G', 'T', 'C'],
+      V: ['G', 'A', 'C'],
+      N: ['G', 'A', 'T', 'C'],
+      I: ['G', 'A', 'T', 'C'],
+    }
+    module_function
+
+    def iupac2normal(seq, prefixes = [''])
+      return prefixes if seq.size == 0
+
+      first = seq[0].to_sym
+      last_seq = seq[1..-1]
+      new_prefixes = []
+      prefixes.each do |prefix|
+        if IUPAC.include?(first)
+          IUPAC[first].each {|base| new_prefixes << "#{prefix}#{base}"}
+        else
+          $stderr.puts "Error: unrecognized base: #{first}"
+          exit
+        end
+      end
+      return iupac2normal(last_seq, prefixes = new_prefixes)
+    end
+
+    def convert_degenerate_primer(primer_file)
+      primer_records = Bio::FlatFile.new(Bio::FastaFormat, File.open(primer_file))
+
+      primer_list = []
+      primer_records.each do |primer|
+        if primer.naseq.to_s =~ /[^atcgATCG]+/
+          normal_seq_list = iupac2normal(primer.naseq.upcase)
+          fasta_io = StringIO.new
+          normal_seq_list.each_with_index do |normal_seq, index|
+            fasta_io << ">#{primer.entry_name}_#{index+1} #{primer.description}\n#{normal_seq}\n"
+          end
+          fasta_io.rewind
+          primer_list += Bio::FlatFile.new(Bio::FastaFormat, fasta_io).to_a
+          fasta_io.close
+        else
+          primer_list << primer
+        end
+      end
+
+      return primer_list
+    end
+
+    # File actionpack/lib/action_view/helpers/text_helper.rb, line 215
+    def word_wrap(text, line_width = 80)
+      text.split("\n").collect do |line|
+        line.length > line_width ? line.gsub(/(.{1,#{line_width}})(\s+|$)/, "\\1\n").strip : line
+      end * "\n"
+    end
+
+    def long_seq_wrap(word, length=80, separator="\n")
+      # Wrap a long sentence with may words into multiple lines
+      (word.length < length) ?
+        word :
+        word.scan(/.{1,#{length}}/).join(separator)
+    end
+
+    def seconds_to_units(seconds)
+      return "#{seconds.round(2)} second" if seconds < 1
+      return "#{seconds.round(2)} seconds" if seconds < 60
+      '%d minutes, %d seconds' %
+      #'%d days, %d hours, %d minutes, %d seconds' %
+      # the .reverse lets us put the larger units first for readability
+
+      #[24,60,60].reverse.inject([seconds]) {|result, unitsize|
+
+      [60].reverse.inject([seconds]) {|result, unitsize|
+        result[0,0] = result.shift.divmod(unitsize)
+        result
+      }
+    end
+
+    def plural_word(word, count)
+      count > 1 ? word + 's' : word
+    end
+
+    def platform_os
+      case RUBY_PLATFORM
+      when /mswin|msys|mingw|cygwin|bccwin|wince|emc/
+        return 'windows'
+      when /darwin|mac/
+        return 'mac'
+      when /linux/
+        return 'linux'
+      when /solaris|bsd/
+        return 'unix'
+      else
+        raise Error::WebDriverError, "Unknown os: #{RUBY_PLATFORM.inspect}"
+      end
+    end
+
+    def platform_bit
+      case RUBY_PLATFORM
+      when /64/
+        return 64
+      when /32/
+        return 32
+      else
+        raise Error::WebDriverError, "Unknown os bit: #{RUBY_PLATFORM.inspect}"
+      end
+    end
+  end
+end
+
+module Bio
+  # A patch for BioRuby FastaFormat class
+  class FastaFormat
+    def entry_name
+      @definition.split.first.chomp(',').gsub(/,/, '.')
+    end
+
+    def description
+      @definition.split[1..-1].join(' ')
+    end
+
+    alias desc description
+  end
+end
+
+# Add the ability to specify switches as required to OptionParser
+class OptionParser
+  
+  # An array of messages describing any missing required switches
+  attr_reader :missing_switches
+  
+  # Convenience method to test if we're missing any required switches
+  def missing_switches?
+    !@missing_switches.nil?
+  end
+
+  # Alias the OptionParser::make_switch function 
+  # (instead of directly modifying it like I did in 0.1.0)
+  alias :pickled_make_switch :make_switch
+  
+  # Wrapper for OptionParser::make_switch to allow for required switches
+  def make_switch(opts, block = nil)
+  
+    # Test if a switch is required
+    required = opts.delete(:required)
+
+    return_values = pickled_make_switch(opts, block)
+
+    # Make sure required switches are given
+    if required 
+      short = return_values[1][0].nil? ? nil : "-#{return_values[1][0]}"
+      long = return_values[2][0].nil? ? nil : "--#{return_values[2][0]}"
+      
+      if !(default_argv.include?(short) || default_argv.include?(long))
+        @missing_switches ||= [] # Should be placed in initialize if incorporated into Ruby proper
+      
+        # Ugly and hard to read, should figure out a prettier way of doing this
+        @missing_switches << "Missing switch: #{short if !short.nil?}#{" or " if !short.nil? && !long.nil?}#{long if !long.nil?}"
+      end
+    end
+    
+    return return_values
+  end
+  
+end

data/lib/qu/utils/version.rb

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+module Qu
+  module Utils
+    VERSION = "1.0.1"
+  end
+end

data/qu-utils.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'qu/utils/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "qu-utils"
+  spec.version       = Qu::Utils::VERSION
+  spec.authors       = ["Wubin Qu"]
+  spec.email         = ["quwubin@gmail.com"]
+  spec.description   = %q{Some useful class or methods}
+  spec.summary       = %q{Utils by Wubin Qu}
+  spec.homepage      = "https://github.com/quwubin/qu-utils"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: qu-utils
+version: !ruby/object:Gem::Version
+  version: 1.0.1
+platform: ruby
+authors:
+- Wubin Qu
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-04-15 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Some useful class or methods
+email:
+- quwubin@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/qu/utils.rb
+- lib/qu/utils/version.rb
+- qu-utils.gemspec
+homepage: https://github.com/quwubin/qu-utils
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0
+signing_key: 
+specification_version: 4
+summary: Utils by Wubin Qu
+test_files: []