iseekwonderful / pypathway Goto Github PK

A Python package should always be able to install itself in an empty virtualenv and handle dependencies automatically. Trying to do this with PyPathway fails:

$ git clone https://github.com/iseekwonderful/PyPathway.git
$ cd PyPathway
$ python3 -m venv build_env
$ source build_env/bin/activate
$ python3 -m pip install -e .
Obtaining file:///opt/repos/PyPathway
    ERROR: Command errored out with exit status 1:
     command: /opt/repos/PyPathway/build_env/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/opt/repos/PyPathway/setup.py'"'"'; __file__='"'"'/opt/repos/PyPathway/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info
         cwd: /opt/repos/PyPathway/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/opt/repos/PyPathway/setup.py", line 8, in <module>
        import numpy
    ModuleNotFoundError: No module named 'numpy'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

This is because numpy is imported before the install_requires directive has a chance to install it.

Hey, I just had a quick question about the SPIA implementation. I noticed that in the tutorial you posted, the p-values for the Colorectal dataset seem to be quite different from the original literature values. For example, pPERT for Alzheimer's Disease is 0.229 in your example but 0.7260 in the original paper by Tarca et al. Is this due to updating of the KEGG database since that paper was published in 2008, or are the datasets used in both cases different?

Thanks!

Hi,
I am using the ora package to perform Reactome and KEGG analyses. I have gene symbols so I used IdMapping to convert them to entrezid. From the conversion I lost a small amount of genes (eg 4 over 1700+ genes in my degs subset).

I performed the analyses both using symbol and entrezid, however I get totally different results. I considered that the loss of genes from the conversion was insignificant to explain these differences, so I was wondering what is the problem.

Thanks