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'IOHandles' object is not subscriptable - cooler 0.9.3 #379

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sebgra opened this issue Jan 26, 2024 · 2 comments · Fixed by #384
Closed

'IOHandles' object is not subscriptable - cooler 0.9.3 #379

sebgra opened this issue Jan 26, 2024 · 2 comments · Fixed by #384

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@sebgra
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sebgra commented Jan 26, 2024 •
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Hello,

We encountered some problems with cooler cload pairs command used like :

cooler cload pairs --zero-based -c1 2 -p1 3 -c2 5 -p2 6 path_to_bins path_to_pairs path_to_cool.

cooler version : 0.9.3
pandas version : 2.0.3

Either we got "'IOHandles' object is not subscriptable" or memory exceeding.

Any tips?

Thanks
@nvictus
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nvictus commented Jan 26, 2024

If you can upgrade to pandas 2.1, does it fix the problem?

@sebgra
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sebgra commented Jan 31, 2024

It has been solved by upgrading pandas!
Thanks a lot!

@sebgra sebgra closed this as completed Jan 31, 2024
@thomas-reimonn thomas-reimonn mentioned this issue Feb 1, 2024
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fix: pandas file handling depending on version open2c/cooler
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@nvictus @sebgra