Add grouping field to CreateGermlines arguments

Issue #111 resolved

nima nouri created an issue 2017-12-13

@javh we may add "fields" arg to CreateGermlines.py like what we have in DefineClones.py...

Comments (7)

Jason Vander Heiden
What would this do?
- 2017-12-13T19:16:21+00:00
nima nouri reporter
-f FIELDS [FIELDS ...] Additional fields to use for grouping. e.g. if there are different subjects in data-set and we want to assign germlines per clone.
- 2017-12-13T19:23:13+00:00
Jason Vander Heiden
Hrm. Not sure that's necessary. Just run it on each file individually? You shouldn't have duplicate clone IDs then.
- 2017-12-13T19:26:02+00:00
nima nouri reporter
True... That is one way, but if user (me) put all the files in one, then it is problematic :)
- 2017-12-13T19:28:48+00:00
Jason Vander Heiden
- changed title to Add grouping field to CreateGermlines arguments
- 2017-12-13T19:29:39+00:00
Jason Vander Heiden
Heh. Then you should probably create a composite clone column in that file anyway, so you don't accidentally merge clones across samples. Eg, db$CLONE=paste(db$SAMPLE, db$CLONE, sep="-").

I mean, if you want to add it, go ahead. It's probably over-engineering though, because there's a simpler solution.
- 2017-12-13T19:32:20+00:00
Jason Vander Heiden
- changed status to resolved
Gonna close this because I think the use case sounds like a bad input file. Reopen if we have a need.
- 2018-03-13T00:40:54+00:00
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