# HG changeset patch
# User estrain
# Date 1646758490 0
# Node ID d57fecce2d3b627fd120d22ba7d0860f85490886
# Parent  9b71d79ff903d3240895474a9fbc5de30b94848b
Uploaded

diff -r 9b71d79ff903 -r d57fecce2d3b data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py
--- a/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py	Tue Mar 08 10:52:29 2022 +0000
+++ b/data_manager_amrfinderplus_database_builder/data_manager/data_manager_amrfinderplus_database_builder.py	Tue Mar 08 16:54:50 2022 +0000
@@ -30,12 +30,12 @@
     for f in files:
       ftp.retrbinary("RETR " + f, open(f, 'wb').write)
 
-    ftp.quit()
-
-    #find species specific point mutation files
+    files = ftp.nlst()
+    files = filter(lambda x: re.search(r'^((?!allele|(?:invokername=allele)).)*$', x), files)
     pointmuts = filter(lambda x: re.search(r'^((?!tab|(?:invokername=tab)).)*$', x), files)
     pointmuts = filter(lambda x: re.search(r'AMR_DNA-', x), pointmuts)
 
+
     # Make blast databases
     blastcmd = "makeblastdb -in AMRProt -dbtype prot -logfile /dev/null"
     os.system(blastcmd)
@@ -43,6 +43,7 @@
     os.system(blastcmd)
 
     for f in pointmuts:
+      print(f)
       blastcmd = "makeblastdb -in " + f +" -dbtype nucl -logfile /dev/null"
       os.system(blastcmd)
 
@@ -54,6 +55,8 @@
     with open("version.txt") as f:
       version = f.readline().rstrip()
 
+    ftp.quit()
+    
     return version 
 
 def print_json (version,argspath):
@@ -65,7 +68,6 @@
         'amrfinder_databases': [
           {
             "value":valueentry,
-            "dbkey":valueentry,
             "name":version,
             "path":argspath,
           }
@@ -90,8 +92,6 @@
     os.chdir("..")
 
     shutil.copytree("output",args.path[0])
-    shutil.rmtree("output")
-
     print_json(version,args.path[0])
 
 if __name__ == "__main__": main()