Feature request: simulate fixed CDR3 length

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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Feature request: simulate fixed CDR3 length #249

Closed scharch closed 5 years ago

scharch commented 6 years ago

Low priority, since I can always filter, but seems like it would be easy to implement and would save computing time for questions where it's relevant.

psathyrella commented 6 years ago

Good idea.

Quick fix: copy your parameter dir, pull up all-probs.csv (full joint counts), and remove all the lines with wrong cdr3. Or, since these are the full rearrangement events, and simulation is basically just choosing lines: just delete/modify it down to the lines (exact rearrangement events) you want.

psathyrella commented 6 years ago

I added the functional columns to default simulation files (as described ^), I'll get to the actual cdr3 filtering somewhat, um, later.