These are chat archives for dereneaton/ipyrad

20th
Feb 2016
Deren Eaton
@dereneaton
Feb 20 2016 17:37 UTC
I'm working on refining preview mode and getting steps 6-7 to work better. I think that will make things feel much more solid. Do you think you could figure out how to reindex the stats dataframes after they'er reloaded from JSON.
Isaac Overcast
@isaacovercast
Feb 20 2016 17:41 UTC
sure, np
Isaac Overcast
@isaacovercast
Feb 20 2016 18:44 UTC
I think we should just eliminate support for the old style .assembly objects. At the same time i prefer load_assembly() to load_json(), makes it more explicit what you want to do? idk wat u think?
Isaac Overcast
@isaacovercast
Feb 20 2016 20:29 UTC
Emailed travis glenn, he's gonna give us some 3rad/radcap data
Deren Eaton
@dereneaton
Feb 20 2016 20:44 UTC
sweet.
and yeah, just wanted to keep load_assembly around long enough for you and glenn to be able to keep your existing data sets alive.
Isaac Overcast
@isaacovercast
Feb 20 2016 20:46 UTC
Oof, in order to solve the key reordering thing i am trying to implement an OrdObjDict, similar to the ObjDict() you have so the can be accessed as attributes.
Deren Eaton
@dereneaton
Feb 20 2016 20:46 UTC
0.1.53 changes look great.
Isaac Overcast
@isaacovercast
Feb 20 2016 20:46 UTC
cool
Deren Eaton
@dereneaton
Feb 20 2016 20:47 UTC
sweet. yeah those custom json hooks are a little tricky.
Isaac Overcast
@isaacovercast
Feb 20 2016 20:48 UTC
so i got data.statsfiles sorting right, and i see that data.samples["1A_0"].statsfiles is also unordered
you mention data.dirs in the ticket, is there a particular order you want to maintain? Also, any other ordering things i'm not thinking of?
Deren Eaton
@dereneaton
Feb 20 2016 20:54 UTC
order: fastq, edits, clusts, consens, outfiles
also the order of the summarized stats in data.stats should start with state and then show results for each of steps 1-5
Isaac Overcast
@isaacovercast
Feb 20 2016 22:15 UTC
I have been beating my head coming up with a tricky technical solution for reordering the keys, but i just now thought of a clever "trick" that might make it a millllion times easier and simpler.
I need to know if this will work for what you need. Instead of getting all fancy with ordered dicts and stuff, which is a true pain, i implemented the repr() function for ObjDict, and inside this function it does the sorting.
Hm, maybe that won't work...
The OrdObjDict road I was taking got really really hairy.
Deren Eaton
@dereneaton
Feb 20 2016 22:36 UTC
one option is to load in the dataframe and then call "reindex" on it
and set the index order
I fixed the LOGGER so it logs within engines again in 0.1.54
Isaac Overcast
@isaacovercast
Feb 20 2016 22:38 UTC
Bless you...
I just pushed a change to ObjDict that properly sorts data.dirs, data.statsfiles, and samples.statsfiles, will you check it out and let me know if that works for what you need?
Isaac Overcast
@isaacovercast
Feb 20 2016 23:10 UTC
samples.stats was much easier to reorder in a straightforward way inside load_json()