Mercurial > repos > estrain > seqsero2_v1_0_1
changeset 32:7c51eb2396a9
Uploaded
| author | estrain |
|---|---|
| date | Sat, 07 Sep 2019 14:48:10 -0400 |
| parents | 564ca9d91226 |
| children | 6d8f3c66a836 |
| files | SeqSero2_package.py |
| diffstat | 1 files changed, 2 insertions(+), 1 deletions(-) [+] |
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--- a/SeqSero2_package.py Sat Sep 07 14:27:42 2019 -0400 +++ b/SeqSero2_package.py Sat Sep 07 14:48:10 2019 -0400 @@ -1214,7 +1214,8 @@ def judge_subspecies(fnameA,dirpath): #seqsero2 -a; judge subspecies on just forward raw reads fastq - salmID_output=subprocess.Popen("python SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) + #salmID_output=subprocess.Popen("python SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) + salmID_output=subprocess.Popen("python "+ dirpath + "/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) salmID_output2=subprocess.Popen("ls",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) out, err = salmID_output.communicate() out2, err2 = salmID_output2.communicate()