Missing required python packages: scipy and pysam

[skchronicles]

Hello there,

Thank you for creating and maintaining this awesome tool!

I ran rMATS, and I am using this package to visualize the results. I installed rmats2sashimiplot in a virtual environment from pypi (v2.0.4). I noticed whilst running the tool, two required python packages were missing: pysam and scipy. These are two packages that are not bundled within the standard library so you may want to add a requirements.txt file and update your setup.py so these packages are automatically downloaded.

Thank you again for this super useful tool.

Best, @skchronicles

[skchronicles]

I just wanted to provide some more information. As there are a few extra dependencies that are not listed. I also found out that matplotlib is an additional python dependency, and that the samtools executable is also a dependency as well. samtools must be in your $PATH prior to running rmats2sashimiplot.

I also ran into another issue when trying to run this tool. I kept getting issues related to the following module being missing: mpl_toolkits.axes_grid.

# Missing module being imported in:
# src/MISO/misopy/sashimi_plot/plot_utils/plotting.py
    from mpl_toolkits.axes_grid.axislines import SubplotZero
ModuleNotFoundError: No module named 'mpl_toolkits.axes_grid'

It is worth noting that I installed this tool in a python3.8 base virtual environment with the provided 2to3.sh script. If you installed this tool, within a python2 environment, you will likely not run into this previous issue. It might be worth updating the tool to permanently use python3, as python2 is past the end of its lifecycle. Anyways, to fix the issue above related to the missing module, mpl_toolkits.axes_grid, I commented out line 5 where the import was occurring and replaced it with this: from mpl_toolkits.axisartist.axislines import SubplotZero.

Here is what the patched src/MISO/misopy/sashimi_plot/plot_utils/plotting.py program looks like:

##
## Plotting utils
##
import matplotlib.pyplot as plt
#from mpl_toolkits.axes_grid.axislines import SubplotZero
from mpl_toolkits.axisartist.axislines import SubplotZero
import scipy.stats as stats
from scipy import *
from numpy import array
from scipy import linalg

I hope this helps anyone else encountering these issues.

Best Regards, @skchronicles