These are chat archives for dereneaton/ipyrad

12th
Feb 2016
Deren Eaton
@dereneaton
Feb 12 2016 00:00
I see
yeah, maybe we just do if '1' in args.steps, and ignore foce
Isaac Overcast
@isaacovercast
Feb 12 2016 00:01
OK.
Re: preview mode, another option is to add a third arg to preview_truncate_fq where you pass in the number of lines to slice off, that way steps 1, 2, and 3 can customize the length of the preview files.
Deren Eaton
@dereneaton
Feb 12 2016 00:04
I thought we only need to truncate 1 and 2.
Isaac Overcast
@isaacovercast
Feb 12 2016 00:08
I could see people wanting to do a full run through step 2, and then wanting to experiment with preview runs of step 3, to tune param settings.
Deren Eaton
@dereneaton
Feb 12 2016 00:09
OK, i could see that. If so, the best approach might be to subsample after de-replicating the reads.
Isaac Overcast
@isaacovercast
Feb 12 2016 00:13
That makes sense... What do you think about adding a 3rd param to preview_truncate_fq? then step2 can call preview_truncate_fq(data, sample.files.fastqs, data._hackersonly["preview_truncate_length"/10), or something like that.
Deren Eaton
@dereneaton
Feb 12 2016 00:18
... I'm not sure, haven't done too much previewing yet, would have to see it in action. But go for it.
Deren Eaton
@dereneaton
Feb 12 2016 17:06
a minor thing, but I think I would prefer to name params files as params-name.txt rather than name-params.txt. That way all of the different params files in a dir would come up next to each other in a terminal, giving a little cleaner feel. yea?
Isaac Overcast
@isaacovercast
Feb 12 2016 17:59
That makes sense, totally.
Deren Eaton
@dereneaton
Feb 12 2016 21:32
I think I've got it figured out how to save assemblies as a JSON dict rather than pickling. It's gonna be soooo much better for allowing changes to Assembly objects.
Deren Eaton
@dereneaton
Feb 12 2016 21:55
the only annoying thing is that json kills tuples and turns them into lists. so there's a bit of work in converting htem back...