changeset 33:ef3f3fd059fa draft

planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit f50ed223904d1471d35d6057a651caf0496d444d-dirty

--- a/data_manager/mob_suite_build_database.py	Wed Jun 26 15:44:07 2019 -0400
+++ b/data_manager/mob_suite_build_database.py	Mon Jul 08 14:36:21 2019 -0400
@@ -5,6 +5,7 @@
 import argparse
 import datetime
 import errno
+import glob
 import json
 import os
 import shutil
@@ -22,19 +23,40 @@
 
     now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
 
-    database_value = str(uuid.uuid4())
+    database_value = str(uuid.uuid1())
 
     database_name = database_name
 
     database_path = database_value
 
+    mob_init_args_list = [
+        '-d', database_path,
+    ]
+
+    subprocess.check_call(['mob_init'] + mob_init_args_list, cwd=target_directory)
+
+    try:
+        os.remove(os.path.join(database_path, "clusters.txt"))
+    except OSError as e:  ## if failed, report it back to the user ##
+        print ("Error: %s - %s." % (e.filename, e.strerror))
+
+    
+    ncbi_plasmid_db_files = glob.glob(os.path.join(database_path, "ncbi_plasmid_full_seqs.*"))
+    for ncbi_plasmid_db_file in ncbi_plasmid_db_files:
+        try:
+            os.remove(ncbi_plasmid_db_file)
+        except OSError as e:
+            print ("Error: %s - %s." % (e.filename, e.strerror))
+
+    
+    
     mob_cluster_args_list = [
         '--num_threads', mob_cluster_args['num_threads'],
         '--infile', mob_cluster_args['infile'],
         '--outdir', database_path,
         '--mode', mob_cluster_args['mode'],
     ]
-
+    
     print(json.dumps(mob_cluster_args_list))
 
     print("Sleeping for 20s")
@@ -46,16 +68,19 @@
     print("Sleeping for 20s")
     time.sleep(20)
     print("Sleep ending")
+
+    shutil.move(os.path.join(database_path, 'references_updated.fasta'),
+                os.path.join(database_path, 'ncbi_plasmid_full_seqs.fas'))
     
     makeblastdb_args_list = [
-        '-in', os.path.join(database_path, 'references_updated.fasta'),
+        '-in', os.path.join(database_path, 'ncbi_plasmid_full_seqs.fas'),
         '-dbtype', 'nucl',
     ]
     
     subprocess.check_call(['makeblastdb'] + makeblastdb_args_list, cwd=target_directory)
 
     mash_sketch_args_list = [
-        '-i', os.path.join(database_path, 'references_updated.fasta'),
+        '-i', os.path.join(database_path, 'ncbi_plasmid_full_seqs.fas'),
     ]
 
     subprocess.check_call(['mash', 'sketch'] + mash_sketch_args_list, cwd=target_directory)