scdataloader 2.0.12__py3-none-any.whl → 2.1.0__py3-none-any.whl

scdataloader/preprocess.py

@@ -264,8 +264,9 @@ class Preprocessor:
         # For genes that are already ENS IDs, use them directly
         prev_size = adata.shape[1]
         # Handle symbol genes
+        cols_to_use = adata.var.columns.difference(genesdf.columns)
         if self.is_symbol:
-            new_var = adata.var.merge(
+            new_var = adata.var[cols_to_use].merge(
                 genesdf.drop_duplicates("symbol").set_index("symbol", drop=False),
                 left_index=True,
                 right_index=True,
@@ -275,7 +276,7 @@ class Preprocessor:
             adata = adata[:, new_var.index]
             new_var.index = new_var["ensembl_gene_id"]
         else:
-            new_var = adata.var.merge(
+            new_var = adata.var[cols_to_use].merge(
                 genesdf, left_index=True, right_index=True, how="inner"
             )
             adata = adata[:, new_var.index]

scdataloader/utils.py

@@ -440,6 +440,7 @@ def load_genes(
         "ncbi_gene_ids",
         "synonyms",
         "description",
+        "abbr",
     ]:
         if col in organismdf.columns:
             organismdf.drop(columns=[col], inplace=True)

{scdataloader-2.0.12.dist-info → scdataloader-2.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scdataloader
-Version: 2.0.12
+Version: 2.1.0
 Summary: a dataloader for single cell data in lamindb
 Project-URL: repository, https://github.com/jkobject/scDataLoader
 Author-email: jkobject <jkobject@gmail.com>
@@ -14,7 +14,7 @@ Requires-Dist: cellxgene-census>=0.1.0
 Requires-Dist: django>=4.0.0
 Requires-Dist: ipykernel>=6.20.0
 Requires-Dist: jupytext>=1.16.0
-Requires-Dist: lamindb[gcp]==2.0.1
+Requires-Dist: lamindb[gcp]==2.1.1
 Requires-Dist: leidenalg>=0.8.0
 Requires-Dist: lightning>=2.3.0
 Requires-Dist: matplotlib>=3.5.0

{scdataloader-2.0.12.dist-info → scdataloader-2.1.0.dist-info}/RECORD

@@ -6,10 +6,10 @@ scdataloader/config.py,sha256=wGlCR3tWyEVa69ajovJKYc86CTCJR8e1xC7BTlUOJQE,34582
 scdataloader/data.py,sha256=9883deD-fA-oS_6USNUokiJuVLLUo7_MsxU3qqwoWlA,25568
 scdataloader/datamodule.py,sha256=pFBGUOHl3ibi8QhiV8x5ukjzVjnJMsZWNw3Ekk3P83Y,43810
 scdataloader/mapped.py,sha256=h9YKQ8SG9tyZL8c6_Wu5Xov5ODGK6FzVuFopz58xwN4,29887
-scdataloader/preprocess.py,sha256=Qxp6JPE-rtwRwO8ju6BbLUIXoDpMu1Qn3lboFNfjywo,40870
-scdataloader/utils.py,sha256=SwiA4CNHRuyx8Pb3Uw2cMPdZidfHoff4smnYyF-bK-g,28312
-scdataloader-2.0.12.dist-info/METADATA,sha256=9nS0CWQ12v_yaEtl6miLt5AXKa1nKWRNV8WjR8oE9aQ,13452
-scdataloader-2.0.12.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-scdataloader-2.0.12.dist-info/entry_points.txt,sha256=VXAN1m_CjbdLJ6SKYR0sBLGDV4wvv31ri7fWWuwbpno,60
-scdataloader-2.0.12.dist-info/licenses/LICENSE,sha256=rGy_eYmnxtbOvKs7qt5V0czSWxJwgX_MlgMyTZwDHbc,1073
-scdataloader-2.0.12.dist-info/RECORD,,
+scdataloader/preprocess.py,sha256=hKnDhZoZkAClZRByOJcvSRykkdY6bhTbIsKge7NV-A0,40964
+scdataloader/utils.py,sha256=4CbcCAR93az4wSVAra8xyOvq01iM57rqCdLbDejj2pw,28328
+scdataloader-2.1.0.dist-info/METADATA,sha256=eHSH7fSk8AofI1fFE4SHXxlACiFS2U7tD16cHApR3hc,13451
+scdataloader-2.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+scdataloader-2.1.0.dist-info/entry_points.txt,sha256=VXAN1m_CjbdLJ6SKYR0sBLGDV4wvv31ri7fWWuwbpno,60
+scdataloader-2.1.0.dist-info/licenses/LICENSE,sha256=rGy_eYmnxtbOvKs7qt5V0czSWxJwgX_MlgMyTZwDHbc,1073
+scdataloader-2.1.0.dist-info/RECORD,,