donovan-h-parks / biolib Goto Github PK

Hi there,

I am currently trying to install compareM.
So I installed biolib before.
Whenever I now try to run compareM, I get
`Traceback (most recent call last):
File "/usr/local/bin/comparem", line 37, in
from comparem.main import OptionsParser
File "/usr/local/lib/python2.7/dist-packages/comparem/main.py", line 33, in
from comparem.plots.heatmap import Heatmap
File "/usr/local/lib/python2.7/dist-packages/comparem/plots/heatmap.py", line 33, in
from biolib.plots.abstract_plot import AbstractPlot
File "/usr/local/lib/python2.7/dist-packages/biolib/plots/abstract_plot.py", line 95
self.logger.error(f'Unrecognized image format: {img_format}')

SyntaxError: invalid syntax `

After going back and forth, no matter if I use pip, pip2 or pip3, always a python3 version gets installed (independent of that it gets installed into python2.7 directories; there is a print statement with brackets in the installed file), whereas compareM seems to expect a python2 version.

The question is: What is wrong, and is it me :/ ?

Greetings,

I am trying to run the DeepTMHMM from Google Colab using the biolib, and it was working smoothly until I started to receive the eternal message "INFO:biolib:Cloud: The job has been queued. Please wait...". My best guess was that I used too large sequence file, however when I tried to use a small file with only 5 proteins, it still never ran.

I am looking forward to use this awesome soft again, but I really do not understand how to make it working :( Thank you in advance for any suggestions.

Sincerely yours,
Daria Dibrova

Greetings!
I noticed that method alphanumeric_sort referred a StackOverflow post, while a recent comment to it noticed that it doesn't work for sorting sets of version numbers alphanumerically; e.g., v1.0.1, v3.5.3, v3.2.4.
I'm trying to learn the usefulness of such small updates on StackOverflow. Would this comment help improve your code? I understand that might not happen in real life situation. In that case, do you think this comment can help prevent future defect (if the code were reused somwhere else)?
I'll really appreciate it if you could kindly give me some feedback or suggestions. Thank you very much for your time.
Have a nice day!