bgyori
commented
3 years ago I couldn't reproduce this issue in a clean Python 3.9 virtualenv so my guess is that the download of the HGNC resource file failed and is truncated, hence the index error. Please try doing the following:
rm ~/.protmapper/0.0.19/hgnc_entries.tsv
python -m protmapper.resourcesYou should then see ~/.protmapper/0.0.19/hgnc_entries.tsv that is about 4.3 MB in size.
eskederks
I ran genewalk from a virtual environment (to avoid conflicting version dependencies) and received the following error (“IndexError”):
Traceback (most recent call last): File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/bin/genewalk", line 5, in
from genewalk.cli import main
File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/lib/python3.9/site-packages/genewalk/cli.py", line 12, in
from genewalk.gene_lists import read_gene_list
File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/lib/python3.9/site-packages/genewalk/gene_lists.py", line 8, in
from indra.databases import hgnc_client, uniprot_client
File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/lib/python3.9/site-packages/indra/databases/uniprot_client.py", line 10, in
from protmapper.uniprot_client import *
File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/lib/python3.9/site-packages/protmapper/init.py", line 16, in
from protmapper.api import ProtMapper, MappedSite
File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/lib/python3.9/site-packages/protmapper/api.py", line 712, in
uniprot_client._build_hgnc_mappings()
File "/software/genewalk/Python-3.9.0-genewalk-1.4.0-venv/lib/python3.9/site-packages/protmapper/uniprot_client.py", line 1221, in _build_hgnc_mappings
uniprot_id = row[6]
IndexError: list index out of range
Any thoughts on why this error arises?