Defense Finder Models

This repository contains MacSyFinder models allowing for a systematic search of anti-phage systems.

The repo is formatted according to MacSyData guidelines and synchronized with macsy-models repository to be available in macsydata.

More information on the systems

To simplify the access to the detection rules of the models we created a table (DefenseFinder_rules.tsv) that recapitulate all the rules of detections for each systems.

For the HMM models, we added the "Liste_hmm_system.md" to give all the threshold used for each models.

More information on the different systems are available on the DefenseFinder wiki.

Modifying the models

To change the models, first create a new remove git branch from master:

git push origin master:<your-branch-name>

Then checkout (= "go to") your branch locally:

git checkout <your-branch-name>

Bring your modifications, then don't forget to check validity of the models:

macsydata check

You can now commit and push:

git status # Visualize which files have changed
git add <the files you want to commit>
git diff --cached # control what you're going to commit
git commit -m 'Fixed the ... model'
git push

The next step is to go to the defense-finder-models Github repository and submit a pull request.

Update the release updates file

Add one line per new system.

Add a column with 0 and 1 for the presence of each system in the new version.

Add one Status_vx.x.x for each system: New, modified, removed or From version vx.x.x (version where the system appears).

Add one column Comment_vx.x.x: with information on the modification or other comment.

Releasing

Once your pull request has been validated and merged, you need to create a release.

Decide of a new version number according to semantic versionning.

Then update the version number in metadata.yml, and merge it to master.

Once you've done this, create a tarball with the following command (don't forget to replace with your version).

tar -czf defense-finder-models-<your-version>.tar.gz \
  ./defense-finder-models/LICENSE \
  ./defense-finder-models/README.md \
  ./defense-finder-models/definitions \
  ./defense-finder-models/metadata.yml \
  ./defense-finder-models/profiles/

Then go to Github. From there, create a new release with the correct version number and the tarball you've just created as attached file.

One you've done this, your new version is discoverable through:

macsydata available --org mdmparis

And you can install it following those lines:

macsydata download --org mdmparis defense-finder-models
macsydata install defense-finder-models-<version>.tar.gz

Or if you're using the mdmparis-defense-finder python package, just run defense-finder update.