Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 24:4e1596ee5c94

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author estrain
date Sat, 07 Sep 2019 13:56:48 -0400
parents f8c06e3b0fb9
children 2bc92eaf2844
comparison
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23:f8c06e3b0fb9 24:4e1596ee5c94
1213 return xmlfile,new_fasta 1213 return xmlfile,new_fasta
1214 1214
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("./SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) 1217 salmID_output=subprocess.Popen("./SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
1218 salmID_output2=subprocess.Popen("ls",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
1218 out, err = salmID_output.communicate() 1219 out, err = salmID_output.communicate()
1220 out2, err2 = salmID_output2.communicate()
1219 out=out.decode("utf-8") 1221 out=out.decode("utf-8")
1222 out2=out2.decode("utf-8")
1220 err=err.decode("utf-8") 1223 err=err.decode("utf-8")
1224 err2=err2.decode("utf-8")
1221 file=open("data_log.txt","a") 1225 file=open("data_log.txt","a")
1222 file.write(out) 1226 file.write(out)
1223 file.close() 1227 file.close()
1224 print("dirpath " + str(dirpath)) 1228 print("dirpath " + str(dirpath))
1225 print("SalmID File" + str(out)) 1229 print("SalmID File" + str(out))
1230 print("SalmID File" + str(out2))
1226 print("SalmID Err File" + str(err)) 1231 print("SalmID Err File" + str(err))
1232 print("SalmID Err File" + str(err2))
1227 print("SalmID 1 "+str(out.split("\n")[1])) 1233 print("SalmID 1 "+str(out.split("\n")[1]))
1228 print("SalmID 0 "+str(out.split("\n")[0])) 1234 print("SalmID 0 "+str(out.split("\n")[0]))
1229 salm_species_scores=out.split("\n")[1].split("\t")[6:] 1235 salm_species_scores=out.split("\n")[1].split("\t")[6:]
1230 salm_species_results=out.split("\n")[0].split("\t")[6:] 1236 salm_species_results=out.split("\n")[0].split("\t")[6:]
1231 max_score=0 1237 max_score=0