comparison bin/SeqSero2_package.py @ 10:e6437d423693 draft

planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty

9:43f6b7f6ebb3

  return xmlfile,new_fasta

def judge_subspecies(fnameA,dirpath):
  #seqsero2 -a; judge subspecies on just forward raw reads fastq
  samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA
  #subprocess.check_call(samid_strcmd + " > Salmidoutput.txt",shell=True)
  print(samid_strcmd)
  salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
  out, err = salmID_output.communicate()
  print("judge_subspecies -> err = salmID_output.communicate() " + err)
  out=out.decode("utf-8")
  file=open("data_log.txt","a")
  file.write(out)
  file.close()
  salm_species_scores=out.split("\n")[1].split("\t")[6:]
  salm_species_results=out.split("\n")[0].split("\t")[6:]

10:e6437d423693

  return xmlfile,new_fasta

def judge_subspecies(fnameA,dirpath):
  #seqsero2 -a; judge subspecies on just forward raw reads fastq
  samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA
  print(samid_strcmd)
  #seqsero2 -a; judge subspecies on just forward raw reads fastq
  #salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
  salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
  out, err = salmID_output.communicate()
  out=out.decode("utf-8")
  print(out)
  print(err)
  file=open("data_log.txt","a")
  file.write(out)
  file.close()
  salm_species_scores=out.split("\n")[1].split("\t")[6:]
  salm_species_results=out.split("\n")[0].split("\t")[6:]