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psathyrella / partis

B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction
GNU General Public License v3.0
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Allow to use annotation output file as input for partitioning #196

Closed psathyrella closed 5 years ago

psathyrella commented 8 years ago

Just need to make sure the annotation output and partition cache file formats are compatible, otherwise the infrastructure's there in --persistent-cachefname.

krdav commented 8 years ago

Yeah that is a good one! The vsearch run would then take no time.

psathyrella commented 8 years ago

note to self: integrate this with #154 and --only-smith-waterman.

psathyrella commented 8 years ago

Spent some time on this last week. It'll be a little more involved than I thought, so unless there's squawking I'm finishing light chains first.

krdav commented 8 years ago

I could add to this that it would also be great if there would be an option to print the annotations when running clustering. This should probably be an easy thing to implement.

psathyrella commented 8 years ago

There totally is! There's an option to print ASCII art annotations (--print-cluster-annotations I think. Better with dark bkg). I think it doesn't write them to csv by default, although it passes them around internally as CSV.

On Aug 11, 2016 4:45 PM, "Kristian Davidsen" notifications@github.com wrote:

I could add to this that it would also be great if there would be an option to print the annotations when running clustering. This should probably be an easy thing to implement.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/psathyrella/partis/issues/196#issuecomment-239316165, or mute the thread https://github.com/notifications/unsubscribe-auth/AC0rc0ke-Fj-XoePe0GQL00WsXNnRaPIks5qe6YigaJpZM4I3jBk .

krdav commented 8 years ago

Thank you, I will try that.

psathyrella commented 5 years ago

This was added a while ago.