qu-cmdwrapper 1.0.0

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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

data/Gemfile

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

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::Cmdwrapper
+
+qu-cmdwrapper: A wrapper for command-line tools, mostly are bioinformatics related tools
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'qu-cmdwrapper'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install qu-cmdwrapper
+
+## Usage
+
+```
+# retrieve sequence from two bit formated database with twoBitToFa command
+amp_seq_list = Cmdwrapper::twoBitToFa(fh.path, db + Qu::Mfeindex::DB_2BIT)
+```
+
+## 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/cmdwrapper.rb

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+require 'qu/utils'
+
+require_relative "cmdwrapper/cmd"
+require_relative "cmdwrapper/version"
+
+module Qu
+  module Cmdwrapper
+    # Your code goes here...
+  end
+end

data/lib/qu/cmdwrapper/cmd.rb

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+#!/usr/bin/env ruby
+
+require 'open3'
+require 'tempfile'
+
+module Qu
+  module Cmdwrapper
+    BIN_ROOT = File.join(__dir__, 'ext_bin')
+    BIN_PATH = File.join(BIN_ROOT, Utils::platform_os, Utils::platform_bit.to_s)
+
+
+    THERMO_PATH = File.join(__dir__, 'primer3_config') + '/'
+
+    module_function
+
+    def primer3_core(p3_input_file)
+      begin
+        cmd = File.join(BIN_PATH, 'primer3_core')
+        begin
+          return system_quietly("#{cmd} #{File.realpath(p3_input_file)}")
+        rescue ShellError
+          return ''
+        end
+      rescue IOError
+        $stderr.puts "Primer3 input file not exists: #{p3_input_file}"
+        exit
+      end
+    end
+
+    def ntthal(s1, s2=nil, mv=50, dv=1.5, d=50, n=0.25, mode='ANY')
+      cmd = File.join(BIN_PATH, 'ntthal')
+      if s2
+        tm = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -r -path #{THERMO_PATH} -a #{mode}`
+      else
+        tm = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -r -path #{THERMO_PATH} -a HAIRPIN`
+      end
+
+      return tm.to_f
+    end
+
+    def faToTwoBit(fasta, twobit)
+      cmd = File.join(BIN_PATH, 'faToTwoBit')
+      `#{cmd} #{fasta} #{twobit}`
+    end
+
+    def twoBitToFa(seq_list_file, twobit_file)
+      cmd = File.join(BIN_PATH, 'twoBitToFa')
+
+      records = []
+      begin
+        out_file = Tempfile.new('twobit')
+        `#{cmd} -seqList=#{seq_list_file} #{twobit_file} #{out_file.path}`
+        out_file.rewind
+
+        Bio::FlatFile.new(Bio::FastaFormat, out_file).each do |record|
+          records << record.naseq.seq
+        end
+      ensure
+        out_file.close
+        out_file.unlink
+      end
+
+      return records
+    end
+
+    def get_binding_seq_list(binding_range_list, twobit_file) 
+      amp_seq_list = []
+      
+      return amp_seq_list if binding_range_list.empty?
+
+      begin
+        fh = Tempfile.new('binding_range_list')
+        fh.write(binding_range_list.join("\n"))
+        fh.close
+        amp_seq_list = twoBitToFa(fh.path, twobit_file)
+      ensure
+        fh.unlink
+      end
+      return amp_seq_list   
+    end
+
+    class ShellError < StandardError; end
+
+    def system_quietly(*cmd)
+      exit_status=nil
+      err=nil
+      out=nil
+      Open3.popen3(*cmd) do |stdin, stdout, stderr, wait_thread|
+        err = stderr.gets(nil)
+        out = stdout.gets(nil)
+        [stdin, stdout, stderr].each{|stream| stream.send('close')}
+        exit_status = wait_thread.value
+      end
+      if exit_status.to_i > 0
+        err = err.chomp if err
+        raise ShellError, err
+      elsif out
+        return out.chomp
+      else
+        return true
+      end
+    end
+
+  end
+end
+
+if $0 == __FILE__
+  puts Qu::Cmdwrapper::BIN_PATH
+end

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