cmapPy/pandasGEXpress/transform_gctoo.py: add code to do transformati…

…ons on GCToo objects for now just transpose

cmapPy/pandasGEXpress/tests/python3_tests/test_transform_gctoo.py

@@ -0,0 +1,41 @@
+
+import unittest
+import logging
+import pandas
+import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_logger
+import cmapPy.pandasGEXpress.GCToo as GCToo
+import cmapPy.pandasGEXpress.transform_gctoo as tg
+
+logger = logging.getLogger(setup_logger.LOGGER_NAME)
+
+
+class TestSubset(unittest.TestCase):
+ def test_transpose(self):
+ data_df = pandas.DataFrame({"a":range(2,5), "b":range(7,10)})
+ logger.debug("happy path - data_df:\n{}".format(data_df))
+
+ row_metadata_df = pandas.DataFrame({"rm1":range(3)}, index=data_df.index)
+ logger.debug("row_metadata_df:\n{}".format(row_metadata_df))
+
+ col_metadata_df = pandas.DataFrame({"cm1":range(2), "cm2":range(3,5)}, index=data_df.columns)
+ logger.debug("col_metadata_df:\n{}".format(col_metadata_df))
+
+ my_gctoo = GCToo.GCToo(data_df, row_metadata_df=row_metadata_df, col_metadata_df=col_metadata_df)
+ logger.debug("my_gctoo:\n{}".format(my_gctoo))
+
+ r = tg.transpose(my_gctoo)
+ logger.debug("result r:\n{}".format(r))
+
+ logger.debug("r.data_df:\n{}".format(r.data_df))
+ self.assertTrue(data_df.equals(r.data_df.T))
+
+ logger.debug("r.row_metadata_df:\n{}".format(row_metadata_df))
+ self.assertTrue(col_metadata_df.equals(r.row_metadata_df))
+
+ logger.debug("r.col_metadata_df:\n{}".format(r.col_metadata_df))
+ self.assertTrue(row_metadata_df.equals(r.col_metadata_df))
+
+
+if __name__ == '__main__':
+ setup_logger.setup(verbose=True)
+ unittest.main()

cmapPy/pandasGEXpress/transform_gctoo.py

@@ -0,0 +1,22 @@
+"""
+transform_gctoo.py
+
+module to contain various transformations of GCToo objects. Initially just transpose.
+
+"""
+import logging
+
+import cmapPy.pandasGEXpress.setup_GCToo_logger as setup_logger
+import cmapPy.pandasGEXpress.GCToo as GCToo
+
+
+logger = logging.getLogger(setup_logger.LOGGER_NAME)
+
+def transpose(my_gctoo):
+ new_gctoo = GCToo.GCToo(
+ data_df=my_gctoo.data_df.T,
+ row_metadata_df=my_gctoo.col_metadata_df,
+ col_metadata_df=my_gctoo.row_metadata_df
+ )
+
+ return new_gctoo