Create data set compatible for qiime 2 in Large subunit ribosomal RNA (28S) SILVA database


(Kohei Takahashi) #1

Hello,

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.

Regards,


(Nicholas Bokulich) #2

Hi @F18D029G,

This is code unrelated to QIIME 2 so I cannot really offer thorough support — the error message says you are missing cogent, so just try pip install cogent to install and that may be all you need…

The end goal is to get your files into the same format as the QIIME-compatible SILVA files here. The release notes on that file — or contacting the SILVA developers for more details — may also get you on the right track.

cc: @SoilRotifer

Good luck!


(Mike Robeson) #3

Hi @F18D029G and @Nicholas_Bokulich,

The simplest and easiest way to get going, is to install QIIME1, and run the scripts through that environment as it contains all of the dependencies you need.

-Cheers!


(Kohei Takahashi) #4

Hi @Nicholas_Bokulich and @SoilRotifer

Thank you for your reply!!
Successful when ran with qiime 1.


(system) #5

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