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openvax / gtfparse

Parsing tools for GTF (gene transfer format) files
Apache License 2.0
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Update read_gtf.py #39

Closed y9c closed 6 months ago

y9c commented 10 months ago

fix palars error

y9c commented 10 months ago

https://github.com/openvax/gtfparse/pull/34

y9c commented 10 months ago

https://github.com/openvax/gtfparse/pull/35

hsn-ylmz commented 9 months ago

polars also change toggle_string_cache(True) to enable_string_cache(True). Can you please change it and update the conda version?

kmlhpk commented 8 months ago

thanks for this @y9c, I applied this patch by hand (as well as the string cache thing that @hsn-ylmz mentioned) and it fixed my issues.

y9c commented 8 months ago

Hi @hsn-ylmz. Thank you for your suggestion. I have updated accordingly. Could you help review and merge this patch?

jdcla commented 6 months ago

@iskandr gtfparse has been broken for polars>v.016.x Polars is currently at v0.19.19. Any change of these patches being implemented soon?

y9c commented 6 months ago

There is also some bugs in the current release. For example, if there is a ";" in the attribute of the record, gtfparse can not parse the file in the correct way.

iskandr commented 6 months ago

Sorry I was missing these notifications and leaving this broken, I'll take a look today.

iskandr commented 6 months ago

Fixed by https://github.com/openvax/gtfparse/pull/42 -- sorry I left this hanging for so long.