Closed jbloom closed 1 year ago
Thanks @jbloom, I will merge RBD library escape and ACE2 affinity repos in the same way once I get back sera selection data later this week.
dms-vep-pipeline-3
I am posting detailed notes for people how to migrate to the new dms-vep-pipeline-3
(version 3.2.2).
You can now enter receptor affinity experiments, and get plots like this one that show how mutations affect receptor affinity. Note that these are present in a separate section called Receptor affinity in the main docs of a repo.
To add receptor affinity, for backwards compatibility the information is added under the keys receptor_selections
and avg_receptor_selections
in your antibody_escape_config.yaml
file as here. Note that the internal terminology still refers to the selections with soluble receptor as "antibody" just like "antibody" is also used as a synonym for serum. Note that you will likely want to change some of the regularization weights and plotting parameters for receptors. For instance, we no longer want to have a nonzero reg_spread_weight
as probably most mutations at a site will not have same effect on receptor.
The code automatically takes care of the adjustment that "escape" from a soluble receptor means decreased affinity for it.
Previously in the heat maps, if a mutation could not have an escape estimated for it (due to insufficient no-antibody counts) it was shown as missing. But actually, there are mutations that we can measure as being functionally deleterious, but we can't measure escape as they don't make functional virus even in no-antibody condition. Now those are shown as grayed out (deleterious) depending on the value of the functional effect slider, so that we can distinguish between non-measured mutations and those just too deleterious to measure escape for but in library. Note we have also added the min_filters
option under plot_hide_stats
that you should use to set minimal filtering (eg, on times_seen
) in order to use a functional effect measurement.
The CSV files with the antibody escape values averaged over selections also now have the per-selection (replicate) values.
There are some tweaks to the internal re-working and output file names that mostly should not affect you except for the following point in the next section
Just pull the latest version of the dms-vep-pipeline-3
(currently 3.2.2) into your repo.
Then since some output file names have changed, you will need to update your .gitignore
to look like the one here plus whatever additional stuff you needed to add for your specific repo.
Then since some output file names have changed, entirely delete your ./results/
and ./docs/
folders after you have updated .gitignore
, re-run pipeline, and commit with new outputs.
@Bernadetadad, this pull request makes some significant updates / changes. It updates to
dms-vep-pipeline-3
version 3.2.2, which has the improvements described in the CHANGELOG here.Briefly:
antibody_escape_config.yaml
and displayed as its own property in the docs. I think this means you can entirely delete your https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS_ACE2_affinity repo once you have merged this and made sure it is OK..gitignore
is also updated.Also, if you merge, do it with the Squash and merge rather than the Merge pull request option in the merge button.