first version of a loom-file to pandas DataFrame method

main_methods.py

+import loompy
+import pandas as pd
+
+
+def loom_to_pandas_df(file_name="testfiles/test.loom"):
+    """
+    :param file_name: the name of the loom file (default is: "testfiles/test.loom")
+    :return: pandas DataFrame
+    """
+    df = pd.DataFrame  # Empty DataFrame - to return in case of wrong formatting
+
+    if file_name[-4:] != ".loom":
+        print(f"{file_name} is not a valid file name. Only use '.loom' files!")
+
+    with loompy.connect(file_name) as ds:
+        try:
+            df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
+        except AttributeError or ValueError or OSError:
+            raise Exception(f"The loom file {file_name} does not exist or has no valid format!")
+
+    return df

testfiles/how_to_fix_loompy_error.md

+https://github.com/slundberg/shap/issues/2909
+
+Add the following to the lines causing the error
+(replacing `@jit`):
+
+        @jit(nopython=True)
\ No newline at end of file

testfiles/loom_test.py

+import loompy
+import pandas as pd
+
+ds = loompy.connect("test.loom")
+df = pd.DataFrame(data=ds[:, :], index=ds.ra.Gene, columns=ds.ca.input_name)
+ds.close()
+
+df.info()
+df.describe()
\ No newline at end of file