Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 32:7c51eb2396a9

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author estrain
date Sat, 07 Sep 2019 14:48:10 -0400
parents 564ca9d91226
children 4fcd9834e66b
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31:564ca9d91226 32:7c51eb2396a9
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) 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)
1218 salmID_output2=subprocess.Popen("ls",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) 1219 salmID_output2=subprocess.Popen("ls",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
1219 out, err = salmID_output.communicate() 1220 out, err = salmID_output.communicate()
1220 out2, err2 = salmID_output2.communicate() 1221 out2, err2 = salmID_output2.communicate()
1221 out=out.decode("utf-8") 1222 out=out.decode("utf-8")
1222 out2=out2.decode("utf-8") 1223 out2=out2.decode("utf-8")