'IOHandles'

[yardenmatok203]

Hey,

When using cool cload pairs, I get the following:

/python3.8/site-packages/cooler/cli/cload.py", line 551, in pairs
f_in = get_handle(pairs_path, mode='r', compression='infer')[0]
TypeError: 'IOHandles' object is not subscriptable

I will be happy for help!

thanks,
yarden

[luoxun-xl]

Hi, I also came across the problem, and the version of Cooler is 0.9.2. However, the error disappears when I downgrade it to v0.9.1. This may be caused by inconsistencies between the pandas version and the cooler version.

And, the below version works,

- python=3.8.17
- cooler=0.9.1
- pandas=1.5.3

[nvictus]

This appears to be due to some behavior in an old pandas version we haven't accounted for.

Upgrading to the latest possible pandas that supports your python version might fix it. If not, please share which version of pandas causes the error, and your python version.

If you can upgrade to pandas >=2, it should work. Note that pandas 2 only works on py38 or later.

[luoxun-xl]

This appears to be due to some behavior in an old pandas version we haven't accounted for.

Upgrading to the latest possible pandas that supports your python version might fix it. If not, please share which version of pandas causes the error, and your python version.

If you can upgrade to pandas >=2, it should work. Note that pandas 2 only works on py38 or later.

Yes, the below version combination also works,

- cooler=0.9.2
- pandas=2.0.3

[yardenmatok203]

thanks!

now I get the following error:

pandas.errors.ParserError: Too many columns specified: expected 3 and found 2

Thanks a lot,
Yarden

[bskubi]

I also ran into this issue with pandas 1.5.1 and cooler 0.9.3. Upgrading to pandas 2.1.2 fixed the problem. Thanks!