Rewrite partis input code

[lauradoepker]

Background: @metasoarous and Duncan have worked really hard to make the CFT data flow better. Something about yaml.

Now, however, we'll need to get @metasoarous 's cooperation in re-writing the ecgtheow file input since we used to use the pandis creation (by @matsen ) that took partis output and transformed it into a healthy fasta file of input sequences for BEAST.

@metasoarous , we'll need the pieces of your code that turn the seed clusters within the best partitions (and best-plus-X partitions, if applicable) into healthy, seed-lineage-pruned fasta files.

When can I sit down with @metasoarous and @dunleavy005 to make this happen?

[metasoarous]

@lauranoges @dunleavy005 What's the status on this? My sense was that you are now using the latest process_partis.py here; Is that correct? Should we close?

[dunleavy005]

Yes, this is fixed.

[metasoarous]

Great!