These are chat archives for dereneaton/ipyrad

3rd
May 2016
Isaac Overcast
@isaacovercast
May 03 2016 00:40
Since the notebook i wrote just opens the raw reads file and randomly grabs x number of reads sometimes something funny can happen. I have seen simulations of 25 where only 24 were recovered, it happens when you just randomly draw two separate reads from the same locus. I haven't done extensive testing but i would estimate this happens <25% of the time.
The other weird thing that can happen is if you draw a simulated read that is somewhat divergent in one individual from the rest then you will it see recover an unequal number of reads across individuals, because it maps this read uniquely, and the rest of the reads at this locus for all the other individuals get denovo'd. This can happen if your smalt mapping sequence similarity arg is too large, though how large is too large is unknown at this time. I have only ever seen this once.
Normally if i get a sim like this i'll just generate a new one and it'll be fixed.
Deren Eaton
@dereneaton
May 03 2016 00:48
I see.
hey, are you going to Evolution this year?
Isaac Overcast
@isaacovercast
May 03 2016 01:59
i've been thinking about it, tho it's getting late in the game... I'm going on a long trip in july (azores, canary islands, portugal) so i think adding another trip in june would crush me, but i kinda want to go... are you?
Deren Eaton
@dereneaton
May 03 2016 02:40
yeah
I'll be doing fieldwork in Mexico from mid May to mid June.
I was thinking we should really try to make a public release before then.
we might not have much time to code in May-July, so we could focus on writing a paper with good examples.
This notebook how has all of the code to simulate RAD data and make pseudo-genomes. It also samples one random read per locus from the first N loci, so it won't sample more than one read from the same locus.
it also runs tests on four data types for denovo and reference assembly.
Isaac Overcast
@isaacovercast
May 03 2016 22:44
Omg dude that rules. Actually automating and testing the results is huge, really smart.
Deren Eaton
@dereneaton
May 03 2016 22:44
the progress bars are looking pretty sharp in the API too :wink2:
dang, readthedocs updated a bunch of junk recently and think it broke our docs build.
for one thing, they're now readthedocs.io, instead of .org. But also the docs are failing.
I'm looking into it.
Isaac Overcast
@isaacovercast
May 03 2016 22:54
:{
That's supposed to be an angry face.
Deren Eaton
@dereneaton
May 03 2016 23:25
uuuugh, the docs haven't successfully built in three weeks.
I can't figure out what changed... but it seems to be a problem with jupyter.
oh shit, I fixed it.
jupyter was missing from the environment.yml file