v1.0.2

Removed -target_only from blastdbcmd causing occasionally the command to end prematurely

.gitignore

@@ -1,2 +1,3 @@
 *.pyc
 *.dev
+.DS_Store

avp

@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+#v1.0.2
 
 from depot.interface import main
 

depot/interface.py

@@ -23,7 +23,7 @@
 from docopt import docopt
 
 def main():
-    args = docopt(__doc__,version='1.0.1', options_first=True)
+    args = docopt(__doc__,version='1.0.2', options_first=True)
     if args['<module>'] == 'prepare':
         import depot.prepare as prepare
         prepare.main()

depot/prepare.py

@@ -237,7 +237,7 @@ def main():
     setblastlog_path = os.path.join(tmp_folder,"setblast.log")
 
     if mode == "blast":
-        blastdbcmd_command = 'blastdbcmd -db '+ config_opts["blast_db_path"] + ' -dbtype ' + dbtype + ' -entry_batch ' +  extract_id_path + ' -target_only -outfmt ">%a@%T\n%s" -logfile ' + setblastlog_path + ' -out ' + setblastfa_path
+        blastdbcmd_command = 'blastdbcmd -db '+ config_opts["blast_db_path"] + ' -dbtype ' + dbtype + ' -entry_batch ' +  extract_id_path + ' -outfmt ">%a@%T\n%s" -logfile ' + setblastlog_path + ' -out ' + setblastfa_path
         subprocess.call(blastdbcmd_command, shell= True)
     else: # GK This is specific to SwissProt for now, have to test for UniProt in the future
         if mode == "sp":