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matsengrp / cft

Clonal family tree
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Repurpose process_partis.py for general use #232

Closed lauradoepker closed 6 years ago

lauradoepker commented 6 years ago

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 whether mutated_invariants are kept or not

metasoarous commented 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.