lib/qu/cmdwrapper/cmd.rb in qu-cmdwrapper-1.0.5 vs lib/qu/cmdwrapper/cmd.rb in qu-cmdwrapper-1.0.7

@@ -1,8 +1,9 @@
 #!/usr/bin/env ruby
 
-require 'open3'
+require "open3"
+
 require 'tempfile'
 require 'qu/utils'
 
 module Qu
   module Cmdwrapper
@@ -12,34 +13,39 @@
 
     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}"
+    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
 
     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}`
         # 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
         lines = out.lines
 
@@ -137,12 +143,20 @@
         fh.unlink
       end
       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
       Open3.popen3(*cmd) do |stdin, stdout, stderr, wait_thread|
         err = stderr.gets(nil)