Comments (3)
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")
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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.
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Related Issues (20)
- parse_gctx takes too much memory when we inquire specific columns and rows HOT 2
- reading gctx from a non-fs file object HOT 1
- Cmap tutorial IPython notebook doesn't open in the browser
- CMap tutorial IPython notebook doesn't open HOT 3
- GCTX parsing is not thread safe.
- 'utf-8' codec Error when parsing gctx HOT 1
- Error in parsing
- Subsetting picks wrong dimension to subset over first HOT 1
- Solving environment: failed
- Bug .GCT written by cmapPy on Windows have inconsistent line endings HOT 4
- Cannot write back GCT file that has been parsed HOT 1
- Python 3.11 version
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- pypi release HOT 1
- Unable to install pypi version of cmappy - no such file or directory 'pytz-2021.1.dist-info/METADATA'' HOT 2
- Error in opening LINCS L1000 .gctx file HOT 1
- API Use Cases
- Parse isnt working when trying to read in cs_sig.gtcx from query results
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