Repository navigation
Error during parsing #67
Description
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
Activity
tnat1031 commentedon Nov 13, 2020
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
LeskosekRok commentedon Nov 13, 2020
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:
fromcmapPy.pandasGEXpress.parse_gct import parse`from cmapPy.pandasGEXpress.write_gct import writeparse("testdata_n1000978.gctx")I get:
(base) C:\Users\Rok\Desktop\hello>D:/anaconda/python.exe c:/Users/Rok/Desktop/gctx/readgcxtx.pyT
he given path to the gct file cannot be found. gct_path: testdatan1000978.gctxTraceback (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 parseraise Exception(err_msg.format(file_path))Exception: The given path to the gct file cannot be found. gct_path: testdatan1000978.gctxLeskosekRok commentedon Nov 14, 2020
OK, so gct files get parsed but not gctx. So the problem probably isn't on the part of the software.