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Remove cell ids from engine

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Previously I just removed them from the driver
This commit is contained in:
Charlotte Weaver
2018-07-06 15:38:42 -07:00
parent e3bf06ca61
commit 354eacc3c8
2 changed files with 5 additions and 15 deletions
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server/app/scanpy_engine/scanpy_engine.py
+4 -12
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@@ -13,12 +13,15 @@ class ScanpyEngine(CXGDriver):
def __init__(self, data, schema=None, graph_method="umap", diffexp_method="ttest"):
self.data = self._load_data(data)
self.schema = self._load_or_infer_schema(data, schema)
self._set_cell_ids()
self._set_cell_names()
self.cell_count = self.data.shape[0]
self.gene_count = self.data.shape[1]
self.graph_method = graph_method
self.diffexp_method = diffexp_method
def _set_cell_names(self):
self.data.obs["cell_name"] = list(self.data.obs.index)
@staticmethod
def _load_data(data):
return sc.read(os.path.join(data, "data.h5ad"))
@@ -32,20 +35,9 @@ class ScanpyEngine(CXGDriver):
data_schema = parse_schema(os.path.join(data, schema))
return data_schema
def _set_cell_ids(self):
self.data.obs["cxg_cell_id"] = list(range(self.data.obs.shape[0]))
self.data.obs["cell_name"] = list(self.data.obs.index)
self.data.obs.set_index("cxg_cell_id", inplace=True)
def cells(self):
return list(self.data.obs.index)
def cellids(self, df=None):
if df:
return list(df.obs.index)
else:
return list(self.data.obs.index)
def genes(self):
return self.data.var.index.tolist()