search

edgardomortiz / fineRADstructure-tools

Tools for data conversion and results visualization for fineRADstructure (http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html)
GNU General Public License v3.0
9 stars 2 forks source link

IndexError: list out of range when converting alleles.loci/ipyrad file #1

Closed kevinmneal closed 6 years ago

kevinmneal commented 6 years ago

Hi,

I'm trying to convert the alleles.loci file from ipyrad 0.7.22 [edit: it's actually 0.7.23], and running finerad_input.py I get this error:

Traceback (most recent call last): File "../fineRADstructure-tools/finerad_input.py", line 181, in <module> main() File "../fineRADstructure-tools/finerad_input.py", line 174, in main pyrad_to_finerad(filename, outfile, minsample) File "../fineRADstructure-tools/finerad_input.py", line 67, in pyrad_to_finerad sample = line.split()[0].strip(">")[:-2] # Sample name does not include last two characters IndexError: list index out of range

Any ideas for a fix? Thanks

edgardomortiz commented 6 years ago

I see, perhaps something changed with the latest version of ipyrad, could you send me the first 10000 lines of your alleles.loci?

kevinmneal commented 6 years ago

Command: python2 finerad_input.py -i nativesocal_min281.alleles.loci -t ipyrad

File is here (it's about 254 MB, unfortunately): [edited]

kevinmneal commented 6 years ago

Just saw your edit, here is the file for the first 10000 lines:

[edited]

edgardomortiz commented 6 years ago

Thanks for reporting the bug, it is fixed now.

Edgardo