Individual scopes include seeds even if non producible or absent from the GSMNs about metage2metabo HOT 3 CLOSED

Commit 9385d2e makes the changes for the computation of individual scopes.

Now if a seed is present in an individual scope, it means the corresponding species has an activated reaction to produce it.

I added a tiny toy dataset that enables checking this behavior.

Also done: stop reading and loading the scope json file in every function: use the dict once and for all.

Remaining to be done:

• tests with the new behavior and the tiny dataset
• have the same seed statuses in cscope
• update existing tests
• update documentation

from metage2metabo.

The way the community scope is currently computed hides the producibility of some seeds by species in community. This is incompatible with the harmonisation of the behaviors wrt seeds that we want, and also it hides interesting information.

Additionally, we do not know which species produces each compound in community. So we cannot directly compare iscopes and cscopes at the level of the organism.

A way to solve both problems is to use miscoto focus to compute the community scope. It will provide the impact of interaction on the scope of each species, and the union of all capabilities in community will form the community scope.

Changes needed for this at the level of Miscoto is to support a LP instance as an input, cf cfrioux/miscoto#17.

However, the changes will not work if a host is given to metage2metabo though. These functionalities are not often used and would deserve an update anyway.

from metage2metabo.

Commit 0e2f531 gives the proper behavior to cscope computation.

Now, a seed becoming producible through community interaction will be returned.
Note however that this behavior is not implemented is a host is given to the programme. The old behavior holds in that case.
If no host, miscoto focus retrieves the community scope, and it also provides the contribution of each species to the community scope. Similarly to individual scopes, the community scope is now also reversed in a json and tsv file in order to facilitate analysis.

Warning: if a seed becomes producible through community interaction, it will nonetheless not be considered as a target during minimal community selection. A dedicated log has been added in the programme. [edit: better log done in commit 8203cc5]

from metage2metabo.