exprmat 0.1.9__tar.gz → 0.1.10__tar.gz

{exprmat-0.1.9 → exprmat-0.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: exprmat
-Version: 0.1.9
+Version: 0.1.10
 Summary: routines to process expression matrices
 Home-page: https://github.com/yang-z-03/exprmat
 Author: Zheng Yang
@@ -30,6 +30,7 @@ Requires-Dist: pynndescent
 Requires-Dist: gseapy
 Requires-Dist: metacells
 Requires-Dist: sh
+Requires-Dist: networkx
 Dynamic: author
 Dynamic: author-email
 Dynamic: home-page

{exprmat-0.1.9 → exprmat-0.1.10}/exprmat/data/geneset.py

@@ -42,9 +42,8 @@ def get_genesets(taxa, name, identifier = 'entrez'):
         gs_desc = filtered[1]
         gs_genes = filtered[2:]
 
-        # translation
-        # gs_genes = translate_id(taxa, gs_genes, idfrom = identifier, keep_nones = False)
-        gene_set[gs_name] = gs_genes
+        if len(gs_genes) > 0:
+            gene_set[gs_name] = list(gs_genes)
     
     genome[taxa]['genesets'][name] = gene_set
     return gene_set
@@ -63,6 +62,7 @@ def translate_id(taxa, genes, idfrom = 'entrez', idto = 'ugene', keep_nones = Tr
         gtable = gtable[['ensembl', 'gene']].copy()
         gtable['ugene'] = gtable.index.tolist()
         gtable.index = gtable['ensembl'].tolist()
+        gtable['uppercase'] = gtable['gene'].str.upper().tolist()
 
         # deduplicate
         gtable = gtable.loc[~ gtable['ensembl'].duplicated(), :].copy()