qu-cmdwrapper 1.0.1 → 1.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.rspec

@@ -0,0 +1,2 @@
+--color
+--format documentation

data/Gemfile

@@ -2,4 +2,5 @@ source 'https://rubygems.org'
 
 # Specify your gem's dependencies in qu-cmdwrapper.gemspec
 gemspec
-gem 'qu/utils'
+gem 'qu-utils'
+gem 'rspec'

data/lib/qu/cmdwrapper/cmd.rb

@@ -2,6 +2,7 @@
 
 require 'open3'
 require 'tempfile'
+require 'qu/utils'
 
 module Qu
   module Cmdwrapper
@@ -27,15 +28,74 @@ module Qu
       end
     end
 
-    def ntthal(s1, s2=nil, mv=50, dv=1.5, d=50, n=0.25, mode='ANY')
+    def ntthal(s1:, s2: nil, mv: 50, dv: 1.5, d: 50, n: 0.25, mode: 'ANY', tm_only: false)
       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}`
+        # tm = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -r -path #{THERMO_PATH} -a #{mode}`
+        # out = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -path #{THERMO_PATH} -a #{mode}`
+        out = system_quietly("#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -path #{THERMO_PATH} -a #{mode}")
       else
-        tm = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -r -path #{THERMO_PATH} -a HAIRPIN`
+        # out = `#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -path #{THERMO_PATH} -a HAIRPIN`
+        out = system_quietly("#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -path #{THERMO_PATH} -a HAIRPIN")
+      end
+
+      begin
+        lines = out.lines
+
+        tm = nil
+        dg = nil
+        if lines.shift =~ /.*dG\s+=\s+(-?\d+\.?\d+)\s+t\s+=\s+(\d+\.?\d+)/
+          dg = $1.to_f / 1000
+          tm = $2.to_f
+        end
+
+        if tm_only
+          return tm
+        end
+
+        lines = lines.map {|line| line.split("\t")[1].chomp}
+
+        if s2
+          seq_1 = ''
+          align = ''
+          seq_2 = ''
+          # puts lines
+          (0...lines[0].size).each do |index|
+            if lines[1][index] != ' '
+              seq_1 << lines[1][index]
+              seq_2 << lines[2][index]
+              align << '|'
+            else
+              align << ' '
+              seq_1 << lines[0][index]
+              seq_2 << lines[3][index]
+            end
+          end
+
+          seq_1.sub!(/\-+$/, '')
+          return tm, dg, seq_1, align, seq_2
+
+        else
+          align = lines[0]
+          seq = lines[1]
+
+          return tm, dg, seq, align
+        end
+
+      rescue Exception => e
+
+        if tm_only
+          return 0
+        else
+          if s2
+            return nil, nil, '', '', ''
+          else
+            return nil, nil, '', ''
+          end
+        end
       end
 
-      return tm.to_f
     end
 
     def faToTwoBit(fasta, twobit)
@@ -105,5 +165,14 @@ module Qu
 end
 
 if $0 == __FILE__
-  puts Qu::Cmdwrapper::BIN_PATH
+
+  p1 = 'tccctcctctacaactACCTCGC'
+  p2 = 'TTGGTCGAGGGGAACAGCAGGT'
+  p3 = 'TGTGTGCAGCTGCTGGTGGC'
+  # p1 = 'act'
+  # p2 = 'ctt'
+  puts Qu::Cmdwrapper::ntthal(s1: p1, s2: p2, tm_only: false)
+  puts Qu::Cmdwrapper::ntthal(s1: p1)
+  puts Qu::Cmdwrapper::ntthal(s1: p2)
+  puts Qu::Cmdwrapper::ntthal(s1: p3)
 end

data/lib/qu/cmdwrapper/version.rb

@@ -1,5 +1,5 @@
 module Qu
   module Cmdwrapper
-    VERSION = "1.0.1"
+    VERSION = "1.0.5"
   end
 end

data/qu-cmdwrapper.gemspec

@@ -21,4 +21,5 @@ Gem::Specification.new do |spec|
   spec.add_runtime_dependency 'qu-utils', '~> 1.0'
 
   spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rspec"
 end

data/spec/qu_cmdwrapper_spec.rb

@@ -0,0 +1,14 @@
+require 'spec_helper'
+describe Qu::Cmdwrapper do
+  it 'should return a list' do
+    p1 = 'tccctcctctacaactACCTCGC'
+    p2 = 'TTGGTCGAGGGGAACAGCAGGT'
+    p3 = 'TGTGTGCAGCTGCTGGTGGC'
+    # p1 = 'act'
+    # p2 = 'ctt'
+    # p Qu::Cmdwrapper::ntthal(s1: p1, s2: p2, tm_only: true)
+    # p Qu::Cmdwrapper::ntthal(s1: p1)
+    # p Qu::Cmdwrapper::ntthal(s1: p2)
+    Qu::Cmdwrapper::ntthal(s1: p3)[-1].should eq '------//-/----\\-\\\\--'
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,9 @@
+require 'bundler/setup'
+Bundler.setup
+
+require 'qu/cmdwrapper' # and any other gems you need
+require 'qu/utils' # and any other gems you need
+
+RSpec.configure do |config|
+  # some (optional) config here
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: qu-cmdwrapper
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.0.5
 platform: ruby
 authors:
 - Wubin Qu
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-30 00:00:00.000000000 Z
+date: 2014-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: qu-utils
@@ -38,6 +38,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  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: A wrapper for command-line tools, mostly are bioinformatics related tools
 email:
 - quwubin@gmail.com
@@ -46,6 +60,7 @@ extensions: []
 extra_rdoc_files: []
 files:
 - ".gitignore"
+- ".rspec"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -100,6 +115,8 @@ files:
 - lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds
 - lib/qu/cmdwrapper/version.rb
 - qu-cmdwrapper.gemspec
+- spec/qu_cmdwrapper_spec.rb
+- spec/spec_helper.rb
 homepage: https://github.com/quwubin/qu-cmdwrapper
 licenses:
 - MIT
@@ -124,4 +141,6 @@ rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: A wrapper for command-line tools
-test_files: []
+test_files:
+- spec/qu_cmdwrapper_spec.rb
+- spec/spec_helper.rb