search

BioSystemsUM / MEWpy

Metabolic Engineering Workbench
https://mewpy.readthedocs.io
GNU General Public License v3.0
37 stars 12 forks source link

gene/reaction essential function problem #28

Closed mkulyashov closed 2 years ago

mkulyashov commented 2 years ago

Hi, mewpy team! I have a problem running gene and reaction essentiality function. I used a GSM model with integrated transcriptomic data using RIPTiDe method. So, the analysis for initial model (without transcriptomics data) showes a list of essential genes and reactions but the list is blanked for the transcriptomics-guided model. Moreover, Cobrapy and Optflux functions for the same analysis returns non-zero list of genes/reactions for the last version of the model. In addition to that, the old mewpy version 0.1.11 found them too. Can you give a cue, where is a problem? Thanks in advance for your reply!

vmspereira commented 2 years ago

Hi @mkulyashov,

Thank you for pointing out this issue. I have just committed a fix to it on the devel branch o MEWpy. You can install the fixed version, for example, using pip as follows:

pip install git+https://github.com/BioSystemsUM/mewpy.git@devel

Please let me know if it does solve the problem in your case. Thank you

mkulyashov commented 2 years ago

Thanks for the prompt reply @vmspereira!
I have installed the fixed version. However, it doesn't result in solution of my issue.

vmspereira commented 2 years ago

Would it be possible for you to send an sbml file for whom this issue happens? You may attach it directly here or send it by mail using the address identified on my GitHub account. Thank you.

mkulyashov commented 2 years ago

Yes, no problem. I sent the file with the model to the email.