You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
So far, labelplacements.py only works for MARdb sequences with valid MMP identifiers (so a taxonomic path can be retrieved from the GTDB database). However, this method prevents cluster assignment to query sequences when reference sequences don't come from MARdb.
To this end, we can create a fake taxopath only containing the cluster name (perhaps additional fields if required, it doesn't matter). Gappa examine assign should then assign clusters to placed queries as if it had a valid taxopath
The text was updated successfully, but these errors were encountered:
So far, labelplacements.py only works for MARdb sequences with valid MMP identifiers (so a taxonomic path can be retrieved from the GTDB database). However, this method prevents cluster assignment to query sequences when reference sequences don't come from MARdb.
This issue will modify:
https://github.com/Robaina/TRAITS/blob/7ca208a0bb593dea9ebec5c20a99877e7d60ad3f/code/phyloplacement/placement.py#L371-L389
to allow taxonomy-free cluster assignment.
To this end, we can create a fake taxopath only containing the cluster name (perhaps additional fields if required, it doesn't matter). Gappa examine assign should then assign clusters to placed queries as if it had a valid taxopath
The text was updated successfully, but these errors were encountered: