These are chat archives for dereneaton/ipyrad

Nov 2017
Nov 09 2017 11:55
Nov 09 2017 13:53
Hi @dereneaton and @isaacovercast!!! I have been trying to run the ABBA-BABA tests based on the cookbook available on Github (cookbook-abba-baba.ipynb). Everything loads and runs correctly until I get to the cell. I keep getting the error below. Any ideas? Thanks in advance!!!
Breanna Sipley
Nov 09 2017 15:34
Hi @dereneaton. I have some 2bRAD data that I am analyzing. My impression from the docs is that ipyrad hasn't been tested much on 2bRAD data. Is this accurate? Do you know of any known issues/ limitations/ potential concerns/ workarounds re: ipyrad on 2bRAD data?
Deren Eaton
Nov 09 2017 16:46
@Wind-ant Did you try running it with the example data set? I was able to reproduce this error by setting the tests attribute to be a list with an empty test bb.tests = [{}]. I think the problem likely has to do with how the tests were setup. Either they were entered improperly by hand, or the .generate_tests_from_tree function was not able to generate any tests that met the constraints listed.
@Breanna_Sipley_twitter We have not worked extensively with 2BRAD data, but it is one of our supported datatypes (datatype='2brad'), which we developed from working with an example data set that someone sent to us. The only real difference is in how it treats searching for and trimming adapters from edges, I believe. I can't think of any particular concerns for analyzing it with ipyrad. Happy to help if you run into any problems.