Mercurial > repos > estrain > seqsero2_v1_0_1

changeset 21:95764a93ed88

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Uploaded
author estrain
date Sat, 07 Sep 2019 13:42:22 -0400
parents b2b1d018b90d
children c0c8cc9a3ddb
files SeqSero2_package.py
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/SeqSero2_package.py	Sat Sep 07 13:42:11 2019 -0400
+++ b/SeqSero2_package.py	Sat Sep 07 13:42:22 2019 -0400
@@ -1214,7 +1214,7 @@
 
 def judge_subspecies(fnameA,dirpath):
   #seqsero2 -a; judge subspecies on just forward raw reads fastq
-  salmID_output=subprocess.Popen(dirpath+"/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+  salmID_output=subprocess.Popen("/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
   out, err = salmID_output.communicate()
   out=out.decode("utf-8")
   err=err.decode("utf-8")