I am analyzing LSU data with Qiime 2.
I need LSU reference data set at 99% from SILVA database, and I checked following thread.
In this thread, it was recommended to convert SILVA to RDP file using python code (https://github.com/mikerobeson/Misc_Code/tree/master/SILVA_to_RDP).
But when I run prep_silva_data.py, I got following error.
$ python prep_silva_data.py SILVA_119_LSURef_tax_silva_full_align_trunc.fasta taxonomy.outfile.txt sequence.outfile.fasta
Traceback (most recent call last):
File “prep_silva_data.py”, line 8, in
from cogent.parse.fasta import MinimalFastaParser
ImportError: No module named ‘cogent’
How can I solve this? Or is there another way to make LSU reference data at 99% for QIIME2?
I use python ver. 3.5.