ImportError: cannot import name 'EmptyDataError'

[Former user]

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)

‌

[Assa Yeroslaviz]

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.