Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 19:e33565b4610c

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Uploaded
author estrain
date Sat, 07 Sep 2019 13:16:43 -0400
parents e1287b36e0d3
children 95764a93ed88
comparison
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18:e1287b36e0d3 19:e33565b4610c
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(dirpath+"/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) 1217 salmID_output=subprocess.Popen(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")
1220 file=open("data_log.txt","a") 1221 file=open("data_log.txt","a")
1221 file.write(out) 1222 file.write(out)
1222 file.close() 1223 file.close()
1223 print("dirpath " + str(dirpath)) 1224 print("dirpath " + str(dirpath))
1224 print("SalmID File" + str(out)) 1225 print("SalmID File" + str(out))
1226 print("SalmID Err File" + str(err))
1225 print("SalmID 1 "+str(out.split("\n")[1])) 1227 print("SalmID 1 "+str(out.split("\n")[1]))
1226 print("SalmID 0 "+str(out.split("\n")[0])) 1228 print("SalmID 0 "+str(out.split("\n")[0]))
1227 salm_species_scores=out.split("\n")[1].split("\t")[6:] 1229 salm_species_scores=out.split("\n")[1].split("\t")[6:]
1228 salm_species_results=out.split("\n")[0].split("\t")[6:] 1230 salm_species_results=out.split("\n")[0].split("\t")[6:]
1229 max_score=0 1231 max_score=0