Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 34:4fcd9834e66b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Sat, 07 Sep 2019 14:52:22 -0400
parents 7c51eb2396a9
children 1afc8c8d16b1
comparison
equal deleted inserted replaced
33:6d8f3c66a836 34:4fcd9834e66b
1212 xmlfile="NA" 1212 xmlfile="NA"
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("python SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
1218 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)
1219 salmID_output2=subprocess.Popen("ls",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
1220 out, err = salmID_output.communicate() 1218 out, err = salmID_output.communicate()
1221 out2, err2 = salmID_output2.communicate()
1222 out=out.decode("utf-8") 1219 out=out.decode("utf-8")
1223 out2=out2.decode("utf-8")
1224 err=err.decode("utf-8") 1220 err=err.decode("utf-8")
1225 err2=err2.decode("utf-8")
1226 file=open("data_log.txt","a") 1221 file=open("data_log.txt","a")
1227 file.write(out) 1222 file.write(out)
1228 file.close() 1223 file.close()
1229 print("dirpath " + str(dirpath))
1230 print("SalmID File" + str(out))
1231 print("SalmID File" + str(out2))
1232 print("SalmID Err File" + str(err))
1233 print("SalmID Err File" + str(err2))
1234 print("SalmID 1 "+str(out.split("\n")[1]))
1235 print("SalmID 0 "+str(out.split("\n")[0]))
1236 salm_species_scores=out.split("\n")[1].split("\t")[6:] 1224 salm_species_scores=out.split("\n")[1].split("\t")[6:]
1237 salm_species_results=out.split("\n")[0].split("\t")[6:] 1225 salm_species_results=out.split("\n")[0].split("\t")[6:]
1238 max_score=0 1226 max_score=0
1239 max_score_index=1 #default is 1, means "I" 1227 max_score_index=1 #default is 1, means "I"
1240 for i in range(len(salm_species_scores)): 1228 for i in range(len(salm_species_scores)):