qu-cmdwrapper 1.0.5 → 1.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 0d16b35f5e3360b91a89327adfa9b5c45f86271f
+  metadata.gz: 22a58735233b9a808b30cbb3ec75c989fba69561
+  data.tar.gz: 76c421d95079d6550aba99429fc53565ff3c2656
 SHA512:
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+  data.tar.gz: f0faea15335157a4766f6eed4a38ed18d398dcfbedcf7e768f63af41a061f4b73296944b7ca36936e3c6552b83498161422d6af934ff4c3b88e5808b960549a7

data/lib/qu/cmdwrapper/cmd.rb

@@ -1,6 +1,7 @@
 #!/usr/bin/env ruby
 
-require 'open3'
+require "open3"
+
 require 'tempfile'
 require 'qu/utils'
 
@@ -14,16 +15,21 @@ module Qu
 
     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}"
+    def primer3_core(paras)
+      cmd = File.join(BIN_PATH, 'primer3_core')
+
+      lines = []
+      paras.each_pair do |key, value|
+        next if value.to_s.empty?
+        lines << "#{key}=#{value}"
+      end
+      lines << "="
+
+      stdout, stderr, status = Open3.capture3(cmd, stdin_data: lines.join("\n"))
+      if status.success?
+        return stdout
+      else
+        $stderr.puts stderr
         exit
       end
     end
@@ -34,10 +40,10 @@ module Qu
       if s2
         # 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}")
+        out = exec_cmd("#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -s2 #{s2} -path #{THERMO_PATH} -a #{mode}")
       else
         # 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")
+        out = exec_cmd("#{cmd} -mv #{mv} -dv #{dv} -d #{d} -n #{n} -s1 #{s1} -path #{THERMO_PATH} -a HAIRPIN")
       end
 
       begin
@@ -139,9 +145,17 @@ module Qu
       return amp_seq_list   
     end
 
-    class ShellError < StandardError; end
+    def exec_cmd(cmd)
+      stdout, stderr, status = Open3.capture3(cmd)
+      if status.success?
+        return stdout
+      else
+        puts stderr
+        exit
+      end
+    end
 
-    def system_quietly(*cmd)
+    def system_quietly_old(*cmd)
       exit_status=nil
       err=nil
       out=nil

data/lib/qu/cmdwrapper/version.rb

@@ -1,5 +1,5 @@
 module Qu
   module Cmdwrapper
-    VERSION = "1.0.5"
+    VERSION = "1.0.7"
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: qu-cmdwrapper
 version: !ruby/object:Gem::Version
-  version: 1.0.5
+  version: 1.0.7
 platform: ruby
 authors:
 - Wubin Qu
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-09 00:00:00.000000000 Z
+date: 2014-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: qu-utils
@@ -137,7 +137,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: A wrapper for command-line tools