Mercurial > repos > estrain > seqsero2_v1_0_1

comparison SeqSero2_package.py @ 23:f8c06e3b0fb9

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author estrain
date Sat, 07 Sep 2019 13:51:19 -0400
parents c0c8cc9a3ddb
children 4e1596ee5c94
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22:c0c8cc9a3ddb 23:f8c06e3b0fb9
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("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 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 err=err.decode("utf-8")
1221 file=open("data_log.txt","a") 1221 file=open("data_log.txt","a")
1222 file.write(out) 1222 file.write(out)