Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 42:1afc8c8d16b1 tip

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author estrain
date Sat, 07 Sep 2019 20:38:09 -0400
parents 4fcd9834e66b
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41:526617c6f359 42:1afc8c8d16b1
1215 def judge_subspecies(fnameA,dirpath): 1215 def judge_subspecies(fnameA,dirpath):
1216 #seqsero2 -a; judge subspecies on just forward raw reads fastq 1216 #seqsero2 -a; judge subspecies on just forward raw reads fastq
1217 salmID_output=subprocess.Popen("python "+ dirpath + "/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) 1217 salmID_output=subprocess.Popen("python "+ dirpath + "/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
1218 out, err = salmID_output.communicate() 1218 out, err = salmID_output.communicate()
1219 out=out.decode("utf-8") 1219 out=out.decode("utf-8")
1220 err=err.decode("utf-8")
1221 file=open("data_log.txt","a") 1220 file=open("data_log.txt","a")
1222 file.write(out) 1221 file.write(out)
1223 file.close() 1222 file.close()
1224 salm_species_scores=out.split("\n")[1].split("\t")[6:] 1223 salm_species_scores=out.split("\n")[1].split("\t")[6:]
1225 salm_species_results=out.split("\n")[0].split("\t")[6:] 1224 salm_species_results=out.split("\n")[0].split("\t")[6:]