Mercurial > repos > estrain > data_manager_fastani

changeset 17:12903778c5ad draft

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Uploaded
author estrain
date Sun, 29 May 2022 23:35:04 +0000
parents e199998ae681
children 734c6e4963a9
files data_manager_fastani/data_manager/data_manager_fastani.py
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_fastani/data_manager/data_manager_fastani.py	Sun May 29 22:30:38 2022 +0000
+++ b/data_manager_fastani/data_manager/data_manager_fastani.py	Sun May 29 23:35:04 2022 +0000
@@ -49,7 +49,8 @@
       'NZ_CP018311':'Vibrio_rotiferianus_strain_B64D1'}
 
     for acc in accdict: 
-      ecmd = "efetch -db nuccore -id " + acc + " -format fasta > " + accdict[acc] + ".fna"
+      cmd = "efetch -db nuccore -id " + acc + " -format fasta > " + accdict[acc] + ".fna"
+      os.system(cmd)
 
     os.chdir(cwd)    
     return 
@@ -93,7 +94,7 @@
       download_D1(output_directory)    
       version="FastANI D1"
     elif(args.type[0]=="VL"): 
-      download_D1(output_directory)    
+      #download_D1(output_directory)    
       download_VL(output_directory)    
       version="FastANI D1 + VetLIRN"