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expasy_enzyme_classes silently drops enzyme classes with non alphanumeric chars in description #310

@wosnat

Description

@wosnat

Describe the bug
A clear and concise description of what the bug is.
In function expasy_enzyme_classes in the file inputs\expasy.py

The regular expression is too restrictive and ignores lines that contain non alphanumeric characters. For example the lines below are quietly ignored because they contain commas (,), semicolons (;) , equal signs (=) etc.:

1.12.98.- With other, known, acceptors.
1.13. -.- Acting on single donors with incorporation of molecular oxygen (oxygenases). The oxygen incorporated need not be derived from O2.
1.14. -.- Acting on paired donors, with incorporation or reduction of molecular oxygen. The oxygen incorporated need not be derived from O2.
1.14.11.- With 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors.
1.14.12.- With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into one donor.
1.14.13.- With NADH or NADPH as one donor, and incorporation of one atom of oxygen.
1.14.14.- With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen.
1.21. -.- Catalyzing the reaction X-H + Y-H = 'X-Y'.
3. 1.13.- Exoribonucleases producing 5'-phosphomonoesters.

To Reproduce
Steps to reproduce the behavior:
from pypath.inputs import expasy
expasy.expasy_enzyme_classes()

look for the enzyme classes listed above.

Expected behavior

All enzyme classes should be returned

Traceback

Log file

Desktop (please complete the following information):

  • OS: WIN11, ubunto
  • Python version: 3.12.11
  • Version or commit hash 0.16.20

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