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ImportError: cannot import name 'EmptyDataError'
Issue #66
new
After successfully completing the mageck count/test steps adn the mageck-vispr snakemake run using the following commands
mageck count --output-prefix results/count/all --norm-method median --list-seq ./library.csv --fastq ../fastq/GSC_0131_Day0_Rep1.fastq.gz ../fastq/GSC_0131_Day0_Rep2.fastq.gz ../fastq/GSC_0131_Day23_Rep1.fastq.gz ../fastq/GSC_0131_Day23_Rep2.fastq.gz --sample-label GSC_0131_Day0_Rep1,GSC_0131_Day0_Rep2,GSC_0131_Day23_Rep1,GSC_0131_Day23_Rep2 --trim-5 AUTO 2> logs/mageck/count/all.log
mageck test --norm-method median --output-prefix results/test/GSC --count-table results/count/all.count.txt --treatment-id GSC_0131_Day23_Rep1,GSC_0131_Day23_Rep2 --control-id GSC_0131_Day0_Rep1,GSC_0131_Day0_Rep2 2> logs/mageck/test/GSC.log
mageck-vispr init GSC
snakemake -j 8 -p Snakefile
I got my GSC.vispr.yaml file.
But when trying to run vispr server results/GSC.vispr.yaml within my conda environment, I get the following error:
$ vispr results/GSC.vispr.yaml
Traceback (most recent call last):
File "/home/yeroslaviz/miniconda3/envs/Alessandra/bin/vispr", line 6, in <module>
from vispr.cli import main
File "/home/yeroslaviz/miniconda3/envs/Alessandra/lib/python3.7/site-packages/vispr/__init__.py", line 12, in <module>
from vispr.results import Screens, Screen
File "/home/yeroslaviz/miniconda3/envs/Alessandra/lib/python3.7/site-packages/vispr/results/__init__.py", line 15, in <module>
from vispr.results import rna
File "/home/yeroslaviz/miniconda3/envs/Alessandra/lib/python3.7/site-packages/vispr/results/rna.py", line 14, in <module>
from pandas.io.common import EmptyDataError
ImportError: cannot import name 'EmptyDataError' from 'pandas.io.common' (/home/yeroslaviz/miniconda3/envs/Alessandra/lib/python3.7/site-packages/pandas/io/common.py)
Comments (2)
-
Account Deleted reporter -
I am not sure if the solution I have found is the right one, but all I did is to comment out line 14 in
rna.py
import pandas as pd # from pandas.io.common import EmptyDataError import numpy as np
Now
vispr
is working. - Log in to comment