Mercurial > repos > jjjjia > cpo_prediction

diff cpo_galaxy_prediction.py @ 23:2cca036ceb91 draft

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planemo upload
author jjjjia
date Wed, 29 Aug 2018 01:42:01 -0400
parents e03c8f2d2629
children e5a7da2239af
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line diff
--- a/cpo_galaxy_prediction.py	Tue Aug 28 23:21:34 2018 -0400
+++ b/cpo_galaxy_prediction.py	Wed Aug 29 01:42:01 2018 -0400
@@ -583,10 +583,10 @@
         resfinderCarbas.append(rFinder[keys])
     for keys in rgiAMR:
         if (rgiAMR[keys].Drug_Class.find("carbapenem") > -1 and rgiAMR[keys].AMR_Gene_Family.find("beta-lactamase") > -1):
-            if (rgiAMR[keys].Best_Hit_ARO not in carbapenamases):
+            if ((rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")") not in carbapenamases):
                 carbapenamases.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")")
         else:
-            if (rgiAMR[keys].Best_Hit_ARO not in amrGenes):
+            if ((rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")") not in amrGenes):
                 amrGenes.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")")
     #endregion