fix ambiguity

DessimozLab · Aug 30, 2024 · 809ad83 · 809ad83
1 parent 19befe4
commit 809ad83
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Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/src/HogProf/lshbuilder.py b/src/HogProf/lshbuilder.py
@@ -172,8 +172,7 @@ def __init__(self,h5_oma=None,fileglob = None, taxa=None,masterTree=None, saving
         else:
             self.HAM_PIPELINE = functools.partial( pyhamutils.get_ham_treemap_from_row, tree=self.tree_string ,  swap_ids=self.swap2taxcode  , 
                                                   orthoXML_as_string = False , reformat_names = self.reformat_names , use_phyloxml = self.use_phyloxml , orthomapper = self.idmapper )         
-
-
+
         self.HASH_PIPELINE = functools.partial( hashutils.row2hash , taxaIndex=self.taxaIndex, treeweights=self.treeweights, wmg=wmg , lossonly = lossonly, duplonly = duplonly)
         if self.h5OMA:
 
@@ -323,7 +322,7 @@ def saver(self, i, q, retq, matq, l ):
                                 h5hashes[taxstr][fam, :] = hashes[fam].hashvalues.ravel()
                                 count += 1
                             if self.fileglob:
-                                if not savedf:
+                                if savedf is not None:
                                     savedf = this_dataframe[['Fam', 'ortho']]
                                 else:
                                     savedf = savedf.append(this_dataframe[['Fam', 'ortho']])
@@ -343,9 +342,6 @@ def saver(self, i, q, retq, matq, l ):
                                     print(savedf)
                                     savedf.to_csv(self.saving_path + 'fam2orthoxml.csv')
                                 save_start = t.time()
-
-
-
                         else:
                             print(this_dataframe)
                     else:

diff --git a/src/HogProf/utils/pyhamutils.py b/src/HogProf/utils/pyhamutils.py
@@ -83,7 +83,9 @@ def orthoxml2numerical(orthoxml , mapper):
     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 , use_phyloxml = False , use_internal_name = True ,reformat_names= False, orthomapper = None ):    
+
+
+def get_ham_treemap_from_row(row, tree , level = None , swap_ids = True , orthoXML_as_string = True , use_phyloxml = False , use_internal_name = True ,reformat_names= False, orthomapper = None ):  
     fam, orthoxml = row
     format = 'newick_string'
     if use_phyloxml: