Merge pull request #17 from lozuponelab/skip_async

Skip async download from kegg

AMON/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.0'
+__version__ = '1.0.1'

AMON/predict_metabolites.py

@@ -268,7 +268,7 @@ def make_enrichment_clustermap(pathway_enrichment_dfs: dict, key, output_loc, mi
 def main(kos_loc, output_dir, other_kos_loc=None, compounds_loc=None, name1='gene_set_1', name2='gene_set_2',
          keep_separated=False, samples_are_columns=False, detected_only=False, rxn_compounds_only=False,
          unique_only=True, ko_file_loc=None, rn_file_loc=None, co_file_loc=None, pathway_file_loc=None,
-         write_json=False):
+         write_json=False, try_async=False):
     # create output dir to throw error quick
     makedirs(output_dir)
     logger = Logger(path.join(output_dir, "AMON_log.txt"))
@@ -285,7 +285,7 @@ def main(kos_loc, output_dir, other_kos_loc=None, compounds_loc=None, name1='gen
     logger['Number of samples'] = len(sample_kos)
     logger['Total number of KOs'] = len(all_kos)
 
-    ko_dict = get_kegg_record_dict(set(all_kos), parse_ko, ko_file_loc)
+    ko_dict = get_kegg_record_dict(set(all_kos), parse_ko, ko_file_loc, try_async=try_async)
     if write_json:
         open(path.join(output_dir, 'ko_dict.json'), 'w').write(json.dumps(ko_dict))
         logger['KO json location'] = path.abspath(path.join(output_dir, 'ko_dict.json'))
@@ -296,7 +296,7 @@ def main(kos_loc, output_dir, other_kos_loc=None, compounds_loc=None, name1='gen
     logger['Total number of reactions'] = len(all_rns)
 
     # get reactions from kegg
-    rn_dict = get_kegg_record_dict(set(all_rns), parse_rn, rn_file_loc)
+    rn_dict = get_kegg_record_dict(set(all_rns), parse_rn, rn_file_loc, try_async=try_async)
     if write_json:
         open(path.join(output_dir, 'rn_dict.json'), 'w').write(json.dumps(rn_dict))
         logger['RN json location'] = path.abspath(path.join(output_dir, 'rn_dict.json'))
@@ -333,7 +333,7 @@ def main(kos_loc, output_dir, other_kos_loc=None, compounds_loc=None, name1='gen
         logger['Number of cos produced and detected'] = len(all_cos_produced)
 
     # Get compound data from kegg
-    co_dict = get_kegg_record_dict(all_cos_produced, parse_co, co_file_loc)
+    co_dict = get_kegg_record_dict(all_cos_produced, parse_co, co_file_loc, try_async=try_async)
     if write_json:
         open(path.join(output_dir, 'co_dict.json'), 'w').write(json.dumps(co_dict))
 
@@ -360,7 +360,7 @@ def main(kos_loc, output_dir, other_kos_loc=None, compounds_loc=None, name1='gen
 
     # Get pathway info from pathways in compounds
     all_pathways = [pathway.replace('map', 'ko') for pathway in get_pathways_from_cos(co_dict)]
-    pathway_dict = get_kegg_record_dict(all_pathways, parse_pathway, pathway_file_loc)
+    pathway_dict = get_kegg_record_dict(all_pathways, parse_pathway, pathway_file_loc, try_async=try_async)
     pathway_to_compound_dict = get_pathway_to_co_dict(pathway_dict, no_glycan=False)
 
     # calculate enrichment

scripts/amon.py

@@ -40,6 +40,9 @@
     parser.add_argument('--pathway_file_loc', help='Location of pathway file from KEGG FTP download')
     parser.add_argument('--save_entries', help='Save json file of KEGG entries at all levels used in analysis for '
                                                'deeper analysis', action='store_true', default=False)
+    parser.add_argument('--download_kegg_async', help='KEGG data should be downloaded in parallel (note: this is '
+                                               'faster for small numbers of KOs but fails with larger numbers '
+                                               'due to KEGG API restrictions', action='store_true', default=False)
 
     args = parser.parse_args()
     kos_loc = args.gene_set
@@ -67,10 +70,11 @@
     co_file_loc = args.co_file_loc
     pathway_file_loc = args.pathway_file_loc
     write_json = args.save_entries
+    try_async=args.download_kegg_async
 
     if detected_compounds_only and detected_compounds is None:
         raise ValueError('Cannot have detected compounds only and not provide detected compounds')
 
     main(kos_loc, output_dir, other_kos_loc, detected_compounds, name1, name2, keep_separated, samples_are_columns,
          detected_compounds_only, rn_compounds_only, unique_only, ko_file_loc=ko_file_loc, rn_file_loc=rn_file_loc,
-         co_file_loc=co_file_loc, pathway_file_loc=pathway_file_loc, write_json=write_json)
+         co_file_loc=co_file_loc, pathway_file_loc=pathway_file_loc, write_json=write_json, try_async=try_async)