These are chat archives for dereneaton/ipyrad

Feb 2019
serena acha
Feb 12 03:41

Hello, I have been trying to run the PCA cookbook in jupyter notebook in my university HPC and I found the following error: Could you please help me? I installed all the dependencies
AttributeErrorTraceback (most recent call last)

<ipython-input-11-6c58a4b84106> in <module>()
----> 1 pca.plot()

/home/brigette.williams/.conda/envs/conda-env/lib/python2.7/site-packages/ipyrad/analysis/pca.pyc in plot(self, pcs, ax, cmap, cdict, legend, title, outfile)
295 self.ncomponents = len(self.samples_vcforder)
296 print(" INFO: # PCs < # samples. Forcing # PCs = {}".format(self.ncomponents))
--> 297 coords, model = allel.stats.pca(allele_counts, n_components=self.ncomponents, scaler='patterson')
299 self.pcs = pd.DataFrame(coords,

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

Feb 12 23:52

@isaacovercast Hi Isaac -- just checking in to see if you've had any luck with the error that @jhoepke @caesantibanez @sandrahoffberg @Jamie_Bio_twitter @twpierson and some others were running into with empty arrays at Step 7. If you have a suggested workaround, even if it's not a full fix, I'd be very grateful! I'll also be interested if you solve the discrepancy between denovo and reference+denovo assemblies. Thanks again.

@tim-oconnor @Jamie_Bio_twitter Yeah, sorry I'm behind on things a bit. This is still on my stack, will try to get to it this week.