cfrioux/miscoto

Python package for large-scale community selection in microbiota

miscoto's Issues

Create a new miscoto tool for dead end and orphan metabolites search in community

Following the issue in AuReMe/metage2metabo#38, a new miscoto could be developed to predict the dead end and the orphan metabolites in a community.

miscoto instance adds the host fact even without host

miscoto instance adds a fact for the host even when it is not given as an argument

https://github.com/cfrioux/miscoto/blob/master/miscoto/miscoto_instance.py#L63

How to specify a particular culture media in the seeds.sbml file ?

Hello,

Is it possible to specify a culture media directly with its biocyc ID in the seeds.sbml file ? Like this one, for example.

Thanks.

Miscoto focus cannot be run from a LP instance

Miscoto mincom and scopes can be run from a pre-computed instance. This is not possible when using miscoto focus, and would be useful for Metage2Metabo (cf issue 53 ).

While making the changes, would make sense to solve #8

PyASP binaries do not install anymore --> 404 not found

Version 1.4.3 Pyasp (major dependency of the package) binaries were removed, creating a 404 not found error at the install step of the packages. Pyasp 1.4.4 (the latest) cannot be used because it does not support latest OS. Plus: Pyasp is archived.
Fix = use https://github.com/aluriak/clyngor and https://github.com/Aluriak/clyngor-with-clingo instead of Pyasp. The last one has strong assets as it installs automatically the binaries of Clingo.
Requires modifications to query.py and meneco.py

Copy but do not modify given instance in miscoto scopes and mincom

If one provides an LP instance in miscoto scopesor miscoto mincom together with seeds and/or targets, they will be added to the end of the instance. We should not modify any of the user's inputs. Instead, we should copy the contents of the instance as a temp file and add the seeds/targets in it. Then remove the temp file at the end of the analysis.

seed

Hi,

Thanks for this pipeline. I am at the same time looking at m2m. I wonder how to generate a "seed" file in .xml especially if I have no idea about the medium that would be used for the community I am working on.
Any suggestions? I am not interested into a specific pathways but more how "my" bacteria community cooperate.
Thanks for your help!

Nico