These are chat archives for dereneaton/ipyrad

14th
Jun 2017
leclearnm
@leclearnm
Jun 14 2017 20:00

Hi @isaacovercast @dereneaton ,
I have a question about the function loci2multinexus.py that is giving me an error while trying to work through the cookbook for running BUCKy in parallel Jupyter Notebook (https://github.com/dereneaton/ipyrad/blob/master/docs/cookbook-bucky.rst)
Specifically I am getting this error when trying to generate the nexus files from the .loci file for a subset of taxa

## create a name for this particular data set
NAME = "loureira"

## create nexus files for this data set
ifc.loci2multinex(name=NAME,
                  locifile=LOCIFILE,
                  minSNPs=2,
                  outdir=WORKDIR,
                  subsamples=SUBSAMPLES)
IndexError                                Traceback (most recent call last)
<ipython-input-32-a8b454f7f3c3> in <module>()
      7                   minSNPs=2,
      8                   outdir=WORKDIR,
----> 9                   subsamples=SUBSAMPLES)

/home/nathan/miniconda2/lib/python2.7/site-packages/ipyrad/file_conversion/loci2multinex.pyc in loci2multinex(name, locifile, subsamples, outdir, maxloci, minSNPs, seed, mcmc_burnin, mcmc_ngen, mcmc_sample_freq)
    106 
    107         ## get names and seq from locus
--> 108         names = [i.split()[0] for i in dat]
    109         seqs = np.array([list(i.split()[1]) for i in dat])
    110 

IndexError: list index out of range

I was able to get the program to run using the pedicularis data set, so it seems to be something to do with my .loci files

Deren Eaton
@dereneaton
Jun 14 2017 20:06
@leclearnm I'll take a look.