Error during parsing

[LeskosekRok]

I'm trying to read a gctx file downloaded from https://clue.io/data. This is my code:

from cmapPy.pandasGEXpress.parse_gct import parse from cmapPy.pandasGEXpress.write_gct import write parse("C:/Users/User/Desktop/gctx/testdatan1000978.gctx")

This is the error: (base) C:\Users\User\Desktop\hello>D:/anaconda/python.exe c:/Users/User/Desktop/gctx/readgcxtx.py The given path to the gct file cannot be found. gct_path: C:/Users/User/Desktop/gctx/testdatan1000978.gctx Traceback (most recent call last): File "c:/Users/User/Desktop/gctx/readgcxtx.py", line 3, in <module> parse("C:/Users/User/Desktop/gctx/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: C:/Users/User/Desktop/gctx/testdatan1000978.gctx

[tnat1031]

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")

[LeskosekRok]

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

[LeskosekRok]

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