fixes to preserve previous parsing syntax w/updated imports

Author: oena

cmapPy/__init__.py

@@ -1,3 +0,0 @@
-from .clue_api_client import *
-from .pandasGEXpress import *
-from .set_io import *

cmapPy/pandasGEXpress/__init__.py

@@ -0,0 +1,3 @@
+import sys
+sys.path.insert(0, "../..")
+from cmapPy.pandasGEXpress.parse import parse as parse

cmapPy/pandasGEXpress/concat_gctoo.py

@@ -128,7 +128,7 @@ def main():
         # Parse each file and append to a list
         gctoos = []
         for f in files:
-            gctoos.append(parse.parse(f))
+            gctoos.append(parse(f))
 
         # Create concatenated gctoo object
         if args.concat_direction == "horiz":

cmapPy/pandasGEXpress/parse.py

@@ -7,12 +7,15 @@
 Note: Supports GCT1.2, GCT1.3, and GCTX1.0 files. 
 """
 import sys
-sys.path.insert(0, "../..")
+sys.path.insert(0, "../../")
 import logging
 from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
 from cmapPy.pandasGEXpress import parse_gct as parse_gct
 from cmapPy.pandasGEXpress import parse_gctx as parse_gctx
 
+import parse_gct as parse_gct
+import parse_gctx as parse_gctx 
+
 __author__ = "Oana Enache"
 __email__ = "[email protected]"
 

cmapPy/pandasGEXpress/parse_gctx.py

@@ -6,7 +6,7 @@
 import numpy as np
 import pandas as pd
 import h5py
-import cmapPy.pandasGEXpress.GCToo as GCToo
+from cmapPy.pandasGEXpress import GCToo as GCToo
 
 __author__ = "Oana Enache"
 __email__ = "[email protected]"

cmapPy/pandasGEXpress/tests/test_write_gctx.py

@@ -1,5 +1,5 @@
 import sys
-sys.path.insert(0, "../../..")
+sys.path.insert(0, "../../../")
 import logging
 from cmapPy.pandasGEXpress import setup_GCToo_logger as setup_logger
 import unittest