Error during parsing about cmappy HOT 3 OPEN

Hi @LeskosekRok, I am wondering if this might be an issue with the file path on windows. As a test, could you try changing directories into the folder with the gctx file, and then trying to read it?

in that case, the call would just be

parse("testdatan1000978.gctx")

from cmappy.

Thanks for the swift reply. I'm not sure what you mean. The script and the gctx file are in the same directory and if I execute the following:

from cmapPy.pandasGEXpress.parse_gct import parse`

from cmapPy.pandasGEXpress.write_gct import write

parse("testdata_n1000978.gctx")

I get:

(base) C:\Users\Rok\Desktop\hello>D:/anaconda/python.exe c:/Users/Rok/Desktop/gctx/readgcxtx.py
The given path to the gct file cannot be found. gct_path: testdatan1000978.gctx
Traceback (most recent call last):
File "c:/Users/Rok/Desktop/gctx/readgcxtx.py", line 3, in <module>
parse("testdatan1000978.gctx")
File "D:\anaconda\lib\site-packages\cmapPy\pandasGEXpress\parse_gct.py", line 131, in parse
raise Exception(err_msg.format(file_path))
Exception: The given path to the gct file cannot be found. gct_path: testdatan1000978.gctx

from cmappy.

OK, so gct files get parsed but not gctx. So the problem probably isn't on the part of the software.

from cmappy.