I am currently re-running some data through the QIIME 2 pipeline and have gotten to the classifier step when I hit a snag. The current version of the Silva Classifier posted to the documents page is not compatible with my current version of QIIME 2 (2020.2) in a conda environment.
As such I decided to create my own classifier using the 138 Silva release and it is not going well. I have unzipped the file (SILVA_138_SSURef_tax_silva_full_align_trunc.fasta) and have vsearch and biopython installed.
I am trying to follow the Mike Robeson code on github (https://github.com/mikerobeson/Misc_Code/tree/master/SILVA_to_RDP) but I do not know enough about python or coding or the general classifier making process itself to understand what I am doing and where I maybe going wrong. I have tried to look through the forum and other resources, but in all honesty they just made me more confused and made me feel more hopeless.
So I am trying to run the very first step of the pipeline (prep_silva_data.py) and I have no idea what I’m doing because I have no idea what this means and Google was not helpful in the least.
from cogent.parse.fasta import MinimalFastaParser
from string import maketrans