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Improvements according to Python 3.6 #1

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Improvements according to Python 3.6 #1

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27 changes: 13 additions & 14 deletions bin/CPC2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,13 @@
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():
Expand All @@ -29,7 +28,7 @@ def __main():
return -1
else:
if not os.path.isfile(options.fasta):
sys.stderr.write("\n[ERROR] %s is not a file\n"%options.fasta)
sys.stderr.write("[ERROR] %s is not a file\n"%options.fasta)
return -1
if options.reverse:
strand = "-"
Expand Down Expand Up @@ -78,7 +77,7 @@ 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:
Expand All @@ -89,7 +88,7 @@ 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
Expand Down Expand Up @@ -245,9 +244,9 @@ def calculate_potential(fasta,strand,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")
ftmp_feat = open(outfile + ".feat","w")
ftmp_svm = open(outfile + ".tmp.1","w")
ftmp_result = open(outfile,"w")
ftmp_result.write("\t".join(map(str,["#ID","transcript_length","peptide_length","Fickett_score","pI","ORF_integrity","coding_probability","label"]))+"\n")
ftmp_result.close()
fickett_obj = Fickett()
Expand Down Expand Up @@ -280,7 +279,7 @@ def calculate_potential(fasta,strand,outfile):
'''
calculate the coding probability using LIBSVM
'''
sys.stderr.write("\n[INFO] Predicting coding potential, please wait ...")
sys.stderr.write("[INFO] Predicting coding potential, please wait ...\n")

'''
set directories and check depending tools existance
Expand All @@ -297,18 +296,18 @@ def calculate_potential(fasta,strand,outfile):
cmd = cmd + app_svm_predict + ' -b 1 -q ' + outfile + '.tmp.2 ' + data_dir + 'cpc2.model ' + outfile + '.tmp.1 &&'
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)
os.system('rm -f ' + outfile + '.tmp.1 ' + outfile + '.tmp.2')
# subprocess.call("Rscript " + outfile + '.r', shell=True)
#except:
# pass
if exitstatus == 0:
rm_cmd = "rm -f " + outfile + '.feat'
commands.getstatusoutput(rm_cmd)
sys.stderr.write("\n[INFO] Running Done!\n")
subprocess.getstatusoutput(rm_cmd)
sys.stderr.write("[INFO] Running Done!\n")
return 0
else:
sys.stderr.write("\n[ERROR] Prediction error!\n")
sys.stderr.write("[ERROR] Prediction error!\n")
return -1

if __name__ == "__main__":
Expand Down
8 changes: 4 additions & 4 deletions bin/compress.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,10 @@ def gz_file(fq_file,mode,level=6):
if fq_file.endswith("gz"):
fq_fp = gzip.open(fq_file,mode+"b",level)
else:
sys.stderr.write("\n[INFO] read file '%s'"%fq_file)
fq_fp = file(fq_file,mode)
sys.stderr.write("[INFO] read file '%s'\n"%fq_file)
fq_fp = open(fq_file,mode)
except:
sys.stderr.write("\nError: Fail to IO file: %s\n"%(fq_file))
sys.stderr.write("Error: Fail to IO file: %s\n"%(fq_file))
sys.exit(1)
return fq_fp

Expand All @@ -23,7 +23,7 @@ def bz2file(f):
if f.endswith("bz2"):
fz = bz2.BZ2File(f)
else:
sys.stderr.write("\nError: Fail to IO file: %s\n"%(f))
sys.stderr.write("Error: Fail to IO file: %s\n"%(f))
sys.exit(1)
return fz

4 changes: 2 additions & 2 deletions bin/seqio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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))