Add python2 backward compatibility and update README.md

README.md

@@ -1,7 +1,8 @@
 CPC2 standalone
 ====
 
-* 2019-11-19 16:50, Yu-jian Kang
+* 2019-11-23 15:30, Yang Ding
+ - Now CPC2 supports both Python 2 and Python 3 (thanks for help from HyperOdin)
 
 1 Pre-requisite:
 ----

bin/CPC2.py

@@ -5,7 +5,10 @@
 import sys
 import os
 import re
-import subprocess
+if (sys.version_info[0] == 2):
+ import commands
+else:
+ import subprocess
 import time
 from optparse import OptionParser,OptionGroup
 import six
@@ -317,7 +320,10 @@ def calculate_potential(fasta,strand,output_orf,outfile):
  cmd = cmd + app_svm_predict + ' -b 1 -q ' + outfile + '.tmp.2 ' + data_dir + 'cpc2.model ' + outfile + '.tmp.out'
  #cmd = cmd + 'awk -vOFS="\\t" \'{if ($1 == 1){print $2,"coding"} else if ($1 == 0){print $2,"noncoding"}}\' ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&'
  #cmd = cmd + 'paste ' + outfile + '.feat ' + outfile + '.tmp.2 >>' + outfile
- (exitstatus, outtext) = subprocess.getstatusoutput(cmd) 
+ if (sys.version_info[0] == 2):
+ (exitstatus, outtext) = commands.getstatusoutput(cmd)
+ else:
+ (exitstatus, outtext) = subprocess.getstatusoutput(cmd)
 
  '''deal with the output'''
  #print outfile + '.tmp.out'
@@ -354,7 +360,10 @@ def calculate_potential(fasta,strand,output_orf,outfile):
  if exitstatus == 0:
  os.system('rm -f ' + outfile + '.tmp.1 ' + outfile + '.tmp.2 ' + outfile + '.tmp.out ' + outfile)
  rm_cmd = "rm -f " + outfile + '.feat'
- subprocess.getstatusoutput(rm_cmd)
+ if (sys.version_info[0] == 2):
+ commands.getstatusoutput(rm_cmd)
+ else:
+ subprocess.getstatusoutput(rm_cmd)
  sys.stderr.write("[INFO] Running Done!\n")
  return 0
  else: