These are chat archives for dereneaton/ipyrad

30th
Jul 2018
Alice
@Alice85809572_twitter
Jul 30 2018 07:25
Hi again, any idea of how to modify the .json file to be able to work for step 3, 4, 5, 6 and 7 on demultiplex files from different directories (i.e. step 1 and 2 had run seperatly for those files)?
Thanks!
tommydevitt
@tommydevitt
Jul 30 2018 15:45

@isaacovercast Thanks. Is the syntax for the ipyrad.plotting module current in the docs? I tried

import ipyrad.plotting as iplot
canvas = iplot.depthplot(all_samps)

But got

AttributeErrorTraceback (most recent call last)

<ipython-input-10-75663078c104> in <module>()
5
6 import ipyrad.plotting as iplot
----> 7 canvas = iplot.depthplot(all_samps)

AttributeError: 'module' object has no attribute 'depthplot'

Isaac Overcast
@isaacovercast
Jul 30 2018 15:46
@Alice85809572_twitter You should use the merge command to join assemblies https://ipyrad.readthedocs.io/tutorial-combining-data.html
In general it is very dangerous to edit the .json file by hand, unless you really know what you're doing or unless you want the assemblies to break ;p
Isaac Overcast
@isaacovercast
Jul 30 2018 15:58
@tommydevitt The plotting module is somewhat 'beta', so it looks like the API is out of sync with reality. iplot.coverageplots.depthplot is where this function lives now, but I haven't tested it, so ymmv.
tommydevitt
@tommydevitt
Jul 30 2018 15:58
@isaacovercast gotcha, thanks.