exprmat 0.1.7__tar.gz → 0.1.9__tar.gz

{exprmat-0.1.7 → exprmat-0.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.7
+Version: 0.1.9
 Summary: routines to process expression matrices
 Home-page: https://github.com/yang-z-03/exprmat
 Author: Zheng Yang

{exprmat-0.1.7 → exprmat-0.1.9}/exprmat/data/geneset.py

@@ -28,8 +28,7 @@ def get_genesets(taxa, name, identifier = 'entrez'):
         lines = gfile.read().splitlines()
     
     gene_set = {}
-    import tqdm
-    for line in tqdm.tqdm(lines, ncols = 80):
+    for line in lines:
         
         if len(line.strip()) == 0: continue
         if line.startswith('#'): continue
@@ -53,6 +52,9 @@ def get_genesets(taxa, name, identifier = 'entrez'):
 
 def translate_id(taxa, genes, idfrom = 'entrez', idto = 'ugene', keep_nones = True):
 
+    if not taxa in genome.keys():
+        get_genome(taxa)
+
     # setup the conversion table cache
     if not 'conversion' in genome[taxa].keys():
 
@@ -86,6 +88,8 @@ def translate_id(taxa, genes, idfrom = 'entrez', idto = 'ugene', keep_nones = Tr
     
     else:
         result = []
+        froms = gtable[idfrom].tolist()
+        tos = gtable[idto].tolist()
         for x in genes:
             if x in froms:
                 t = tos[froms.index(x)]

exprmat-0.1.9/exprmat/data/hsa/taxa

@@ -0,0 +1 @@
+9606