Closed lauradoepker closed 6 years ago
This has proved to be quite a bit more involved than I expected. There were a lot of weird assumptions in the way it was originally written which made changes around selecting a particular partition/cluster quite onerous, and I ultimately ended up rewriting some sizable chunks of code. On the bright side, things are much better organized now, and I've been able to remove a bunch of old crud; All in all, I'm feeling much better about others using this code now.
Right now I'm just finishing up a few final details with respect to how you select partitions clusters which will make it a little easier to select for different clusters in different ways. Once I'm done with that I'll push.
Please alter
process_partis.py
script to include flags that allow user to manipulate output of healthy sequences (for ecgtheow use).@metasoarous will continue to use that many output files.
We (I, @dunleavy005, and @matsen ) will run this script independently and use the .fasta output file while ignoring the rest.
@metasoarous please include flags that allow us to: choose whether
indel_reversed_seqs
are used or not choose whethermutated_invariants
are kept or not