Filter cluster output - Githubissues

trvrb commented 5 years ago

@miparedes @cassiawag ---

Could you add two command line options to extract_cluster_fastas.py? These are:

--min-size: Take a parameter for the minimum number of genomes to include in an output cluster. I expect this will usually be set to --min-size 2. A lot of the downstream machinery will break if there's just a single sample (ie I expect augur tree to break if handed a FASTA alignment with just a single element).
--filter-to-seattle: It should make life easier downstream if we only export cluster FASTAs that contain "seattle" viruses. You'll need to identify clusters that contain viruses with region: seattle by importing the metadata tsv.

I'd suggest doing these as two separate feature branches / PRs.

cassiawag commented 5 years ago

--min-size is done!

trvrb commented 5 years ago

The use of --min-size is causing an issue with Snakemake if cluster0.fasta is deleted. I think I'd modify extract_cluster_fastas.py to renumber cluster FASTAs to run contiguously from cluster1.fasta, cluster2.fasta, etc...

cassiawag commented 5 years ago

Do you mean to renumber them after the small clusters are dropped due to --min-size?

trvrb commented 5 years ago

@cassiawag: Changes in 1ca1ea21bf765e7fb7560175209c5ec817a749fc have obviated the need for this renumbering. We're no longer relying on the existence of cluster0.fasta.

@miparedes: I made some changes to extract_cluster_fastas.py in the above. You may want to move your changes to be on top of the current master branch.

trvrb commented 5 years ago

This is resolved via #4 and #12.

seattleflu / augur-build

Filter cluster output #3