These are chat archives for dereneaton/ipyrad

Sep 2017
Deren Eaton
Sep 22 2017 14:32
Hi @ahaponski_twitter , did you enter the .loci file as the data argument?
Hi @vieves, we don't have a formal way of doing this, no. One approach would be to make a psuedo-reference genome from the RAD loci you are interested in capturing, and then running the new samples through the reference assembly method so that the results will only be kept if they match to the reference. This is a bit hackish, though.
Amanda Haponski
Sep 22 2017 16:01

Hi @dereneaton . Yes I did enter the .loci file as the data argument. I've tried generating the tests based on a tree as well as creating objects (e.g., aa, bb, cc) and assigning tests to them. Here's the code for generating tests from the tree:

locifile = "90barcode0-75-nocontrols.loci"
newick = "90barcode0-75-nocontrols-mltree-3apr2017-newick"
bb = ipa.baba(data=locifile, newick=newick)
        "p4": ["PHTM"],
        "p3": ["PHTH2R3", "60a1"],

I was wondering if it's just the installation on my machine. Do you have a test dataset I could run?

Deren Eaton
Sep 22 2017 18:47
@ahaponski_twitter You can assemble one of the test data sets from the documentation (, the introductory one should take only about a minute to assemble. Or you can download a working .loci file here (), and pull in names from that. Be sure to update to the latest version if your ipyrad is older. Current is 0.7.13.
Amanda Haponski
Sep 22 2017 20:19
@dereneaton Thank you!!! I assembled the data from tutorial 1 and it worked perfectly. I did get my dataset to work. I have paired end ddRAD data that I generated in v0.5.15 and it appears that the 'nnnn' separating the forward and reverse reads as well as the loci not being numbered consecutively were causing the errors.
Deren Eaton
Sep 22 2017 21:37
oh, great! Good to know.