fixed lshbuilder and flags

src/HogProf/lshbuilder.py

@@ -417,7 +417,7 @@ def main():
     parser.add_argument('--outfolder', help='folder for storing hash, db and tree objects' , type = str)
     parser.add_argument('--lossonly', help='only compile loss events' , type = bool)
     parser.add_argument('--duplonly', help='only compile duplication events' , type = bool)
-    parser.add_argument('--taxcodes', help='use taxid info in HOGs' , type = bool)
+    parser.add_argument('--taxcodes', help='use taxid info in HOGs' , type = str)
     parser.add_argument('--verbose', help='print verbose output' , type = bool)
     dbdict = {
         'all': { 'taxfilter': None , 'taxmask': None },
@@ -475,10 +475,8 @@ def main():
         duplonly = args['duplonly']
     else:
         duplonly = False
-
-
-
-    if args['taxcodes'] == 'True':
+
+    if args['taxcodes']=='True':
         taxcodes = True
     else:
         taxcodes = False

src/HogProf/utils/pyhamutils.py

@@ -33,6 +33,7 @@ def switch_name_ncbi_id(orthoxml , mapdict = None  ):
 
     orthoxml = ET.tostring(root, encoding='unicode', method='xml')
     return orthoxml
+
 def get_ham_treemap_from_row(row, tree , level = None , swap_ids = True , orthoXML_as_string = True ):
     fam, orthoxml = row
     if orthoxml:
@@ -43,11 +44,14 @@ def get_ham_treemap_from_row(row, tree , level = None , swap_ids = True , orthoX
             else:
                 quoted = True
             ham_obj = pyham.Ham(tree, orthoxml, type_hog_file="orthoxml" , tree_format = 'newick_string'  ,use_internal_name=True, orthoXML_as_string=orthoXML_as_string )
+
             tp = ham_obj.create_tree_profile(hog=ham_obj.get_list_top_level_hogs()[0])        
             return tp.treemap
         except:
             print('error' , traceback.format_exc()) 
             return None 
+
+
 def yield_families(h5file, start_fam):
     """
     Given a h5file containing OMA server, returns an iterator over the families