Merge pull request (python3 support) from HyperOdin-master

Changes:

1. all usages of python 2-"file"'s are replaced with python 3-
   "open"'s
2. import six for python 2 and 3 compatibility
3. replace python 2-commands module with python 3-subprocess
   module
4. replace python 2-"print x" with python 3-"print (x)"

Author: yangdingyangding

bin/CPC2.py

@@ -5,14 +5,13 @@
 import sys
 import os
 import re
-import commands
+import subprocess
 import time
 from optparse import OptionParser,OptionGroup
-
+import six
 import numpy as np
 from Bio.Seq import Seq
 from Bio.SeqUtils import ProtParam
-
 import seqio
 
 def __main():
@@ -85,7 +84,7 @@ def find_longest_in_one(self,myframe,direction,start_codon,stop_codon):
 		'''
 		while True:
 			try: 
-				codon,index = triplet_got.next()
+				codon,index = next(triplet_got)
 			except StopIteration:
 				break 
 			if codon in starts and codon not in stops:
@@ -96,7 +95,7 @@ def find_longest_in_one(self,myframe,direction,start_codon,stop_codon):
 				end_extension = False
 				while True:
 					try: 
-						codon,index = triplet_got.next()
+						codon,index = next(triplet_got)
 					except StopIteration:
 						end_extension = True
 						integrity = -1
@@ -252,9 +251,12 @@ def calculate_potential(fasta,strand,output_orf,outfile):
 	'''
 	strinfoAmbiguous = re.compile("X|B|Z|J|U",re.I)
 	ptU = re.compile("U",re.I)
-	ftmp_feat = file(outfile + ".feat","w")
-	ftmp_svm = file(outfile + ".tmp.1","w")
-	ftmp_result = file(outfile,"w")
+## merged by Yang Ding on 2019-11-23
+## 1. all python 2-"file"'s are replaced with python 3-"open"'s
+## 2. keep kangyj's check on output_orf
+	ftmp_feat = open(outfile + ".feat","w")
+	ftmp_svm = open(outfile + ".tmp.1","w")
+	ftmp_result = open(outfile,"w")
 	if output_orf == 1:
 		my_header = ["#ID","transcript_length","peptide_length","Fickett_score","pI","ORF_integrity","ORF_Start","coding_probability","label"]
 	else:
@@ -315,7 +317,7 @@ 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) = commands.getstatusoutput(cmd)	
+	(exitstatus, outtext) = subprocess.getstatusoutput(cmd)	
 
 	'''deal with the output'''
 	#print outfile + '.tmp.out'
@@ -352,7 +354,7 @@ 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'
-		commands.getstatusoutput(rm_cmd)
+		subprocess.getstatusoutput(rm_cmd)
 		sys.stderr.write("[INFO] Running Done!\n")
 		return 0
 	else:

bin/compress.py

@@ -11,7 +11,7 @@ def gz_file(fq_file,mode,level=6):
 			fq_fp = gzip.open(fq_file,mode+"b",level)
 		else:
 			sys.stderr.write("[INFO] read file '%s'\n"%fq_file)
-			fq_fp = file(fq_file,mode)
+			fq_fp = open(fq_file,mode)
 	except:
 		sys.stderr.write("Error: Fail to IO file: %s\n"%(fq_file))
 		sys.exit(1)

bin/seqio.py

@@ -162,8 +162,8 @@ def gtf_parse(fn,add="chr"):
 
 if __name__ == "__main__":
 	a = [[1,10],[17,22],[40,44],[42,47],[46,100],[101,408]]
-	print a
-	print merge_region(a)
+	print (a)
+	print (merge_region(a))