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Following tutorial yields error #32
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Overlooked the need for a very specific Python 2.7 environment (outlined in https://clue.io/cmapPy/build.html#install - and exceeding the information provided in readme - and being inconsistent with tutorial by leading to the setup of a cmappy version that would require To add to confusion the file names had changed between the tutorial and the public version of GSE70138 (which could have opened the possibility for a change of the file format ..). |
Hi @tstoeger, sorry you had difficulties in using the tutorial. If you have suggestions as to how to make installation instructions more clear, feel free to let us know; the README currently links out to ReadTheDocs in order to help us keep documentation in a centralized place and (hopefully) up to date. Regarding the tutorial, I'll update the inconsistencies regarding use of |
Hi @oena ; Let me thank you at first - both for your inquiry, and the already existing documentation of cmapPY, which already has been very useful. Indeed the tutorial is a very nice extra. My troubles had arisen from running into slightly different problems, and noticing that at least three distinct aspects seemed to have changed (version of used dataset, something related to external Python code, something related to cmapPY); As I'd take the tutorial as reference, this would hint at me overlooking something - but also not knowing for sure, which aspect I should trust or follow. Possibly, the tutorial could:
|
Those points all seem very reasonable to me, thanks! I'll see what we can do to address them better than we do currently. |
Hi, |
I made a Python 3 compatible version of cmapPy; Credits for identifying critical section go to @heltena In my usage scenario a single line addition was sufficient.
My usage scenario was restricted to gctx files, which simplifies the problem of Python 3 compatibility. I didn’t check definition of gctx regarding future compatibility of encoding.I have only constructed tests with GSE92742 level 5, and I additionally bypassed GCToo instances as output I have always been only using the data frame contained within them (hence, I did not check their creation for compatibility with Python3). The above covers my usage of cmapPy. |
Hi @benanbardak |
Firstly thank you for response, |
That is a 48 GB file so I will take some time to try to download it. I tried it with another file from the same series "GSE92742_Broad_LINCS_Level2_GEX_delta_n49216x978.gctx.gz" and metadata parsing is working in python2. |
And please check your email.. @tstoeger |
@saksham219 I tried to run tutorial with this data "GSE92742_Broad_LINCS_Level2_GEX_delta_n49216x978.gctx.gz". But again I get an same error. How can I solve this problem? What does mean "the issue might be with your version of cmapPy. " How can I fixed version of cmapPy? |
@benanbardak What I mean is that you might not be using the latest version on the master branch of this repo.
and then trying to read the file again in a new python environment. If the problem still persists, it would be helpful if you could list down the versions of the packages in your python by |
Following the tutorial cmapPy_pandasGEXpress_tutorial.ipynb currently (2018-March-03) yields an error.
Since it uses an external data set GEO GSE70138 (rather than a test contained within cmapPy) it isn't clear, if this error reflects upon an update or problem within cmapPy, the tutorial, or GSE70138. (Besides not being able to follow a tutorial, this error hence makes it difficult for new users to become familiar with gctx files / cmapPy.)
works: upper part of tutorial
number of samples treated with vorinostat: 210
---- show first ones for debugging ----
LJP007_A375_24H:A03
LJP007_A549_24H:A03
LJP007_ASC.C_24H:A03
LJP007_ASC_24H:A03
LJP007_CD34_24H:A03
creates error: loading of records
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