Merge pull request #25 from ryanjameskennedy/dev

Add --save_dbs arg to cli

README.md

@@ -36,7 +36,7 @@ jasentool convert [-i INPUT_FILE [INPUT_FILE ...]] -o OUTPUT_FILE [-f OUT_FORMAT
 
 ### Converge tuberculosis mutation catlogues
 ```
-jasentool converge --output_dir OUTPUT_DIR
+jasentool converge --output_dir OUTPUT_DIR [--save_dbs]
 ```
 
 ### Extract QC values after alignment

jasentool/cli.py

@@ -164,6 +164,11 @@ def __combined_output(group):
     group.add_argument('--combined_output', dest='combined_output', action='store_true',
                        help='combine all of the outputs into one output')
 
+def __save_dbs(group):
+    """Save all intermediary dbs created for TBProfiler db convergence"""
+    group.add_argument('--save_dbs', dest='save_dbs', action='store_true',
+                       help='save all intermediary dbs created for TBProfiler db convergence')
+
 def __sample_sheet(group, required):
     """Add sample_sheet argument to group"""
     group.add_argument('--sample_sheet', required=required, dest='sample_sheet',
@@ -262,6 +267,7 @@ def get_main_parser():
     with subparser(sub_parsers, 'converge', 'Converge TB mutation catalogues') as parser:
         with arg_group(parser, 'optional arguments') as group:
             __output_dir(group, required=False)
+            __save_dbs(group)
             __help(group)
 
     with subparser(sub_parsers, 'qc', 'Run qc on bwa alignment') as parser:

jasentool/converge.py

@@ -59,7 +59,7 @@ def rm_intermediary_files(self):
             elif os.path.isdir(filepath):
                 shutil.rmtree(filepath)
 
-    def run(self):
+    def run(self, save_all_dbs):
         """Run the retrieval and convergance of mutation catalogues"""
         utils = Utils()
         # Download the genome
@@ -86,4 +86,5 @@ def run(self):
         dfs_to_converge = [intersection_df, unique_tbdb_df, unique_who_df, fohm_df]
         converged_df = pd.concat(dfs_to_converge, ignore_index=True).drop_duplicates()
         converged_df.to_csv(self.convereged_outfpath, index=False)
-        self.rm_intermediary_files()
+        if not save_all_dbs:
+            self.rm_intermediary_files()

jasentool/main.py

@@ -134,7 +134,7 @@ def fix(self, options):
     def converge(self, options):
         """Execute convergence of mutation catalogues"""
         converge = Converge(options.output_dir)
-        converge.run()
+        converge.run(options.save_dbs)
 
     def qc(self, options):
         """Execute retrieval of qc results"""