Closed msbentsen closed 2 years ago
Thank you for using GOA TOOLs in your day-to-day work and for taking your time to write us.
I have augmented the test, tests/test_i147_all_taxids.py
so that it always downloads NCBI's gene2go annotation file for better testing, but am not able to duplicate what you are seeing. So we need more information.
In the meantime, here are a couple things to try:
from os import getcwd
from os.path import join
from goatools.base import download_ncbi_associations
fin_anno = join(getcwd(), 'gene2go')
download_ncbi_associations(fin_anno)
$ wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
$ gunzip gene2go.gz
Hi, thank you for getting back to me. I tried the second option, and I think it might be a system-specific issue on my end. I get an "invalid compressed data--format violated" error from gunzip, but I was able to download it from https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
and unzip without issue. So probably something to do with restrictions on downloading from ftp - not quite sure. But my problem was solved, thank you!
Hi,
Thank you for this great package! It has worked for me in the past, but lately I get an error when trying to download the NCBI associations as seen here:
This produces the error:
It seems to be correctly downloading the .gz file, but reading it fails, and so the gene2go-file is empty:![image](https://user-images.githubusercontent.com/47495444/139033374-2607e9e4-eeca-4cfe-8f00-aeaf80106219.png)
If I use an old gene2go file, it works perfectly (I have one from 10.11.2020 which works), but it seems that any new download fails.
I am running
python==3.7.6
andgoatools==1.1.6
on a Debian system.Thank you for any help you might be able to provide for solving this!