adding window size and threshold fix

flatironinstitute · Aug 20, 2021 · cb06489 · cb06489
1 parent 70bf139
commit cb06489
Showing 1 changed file with 14 additions and 4 deletions.
diff --git a/inferelator_prior/network_from_motifs.py b/inferelator_prior/network_from_motifs.py
@@ -116,13 +116,23 @@ def parse_common_arguments(args):
     _intergenic = args.intergenic if args.intergenic is not None else False
 
     if _species is None:
-        _window = args.window_size if args.window_size is not None else DEFAULT_WINDOW
+        try:
+            _window = args.window_size if args.window_size is not None else DEFAULT_WINDOW
+            _use_tss = args.tss
+        except AttributeError:
+            _window, _use_tss = None, None
+
         _tandem = args.tandem if args.tandem is not None else DEFAULT_TANDEM
-        _use_tss = args.tss
     else:
-        _window = SPECIES_MAP[_species]['window'] if args.window_size is None else args.window_size
+        try:
+            _window = SPECIES_MAP[_species]['window'] if args.window_size is None else args.window_size
+            _use_tss = SPECIES_MAP[_species]['use_tss'] if args.tss else args.tss
+        except AttributeError:
+            _window, _use_tss = None, None
+
         _tandem = SPECIES_MAP[_species]['tandem'] if args.tandem is None else args.tandem
-        _use_tss = SPECIES_MAP[_species]['use_tss'] if args.tss else args.tss
+
+
 
     # Load gene and regulator lists
     _gl = pd.read_csv(args.genes, index_col=None, header=None)[0].tolist() if args.genes is not None else None