Fix error with biopython 1.81 #137
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| @@ -69,7 +77,7 @@ def _split_keyvals(keyval_str): | |||
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| GFF3 has key value pairs like: | |||
| count=9;gene=amx-2;sequence=SAGE:aacggagccg | |||
| GFF2 and GTF have: | |||
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If you don't use auto-formatting your PR would be easier to review! Thanks for giving this a stab!
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yeah, sorry, I figured auto-formatting is enabled everywhere by default now anyway, and the diff is not so huge
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ping @chapmanb in case you were not notified :) |
MatBarba
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Pending BCBio fix: chapmanb/bcbb#137
MatBarba
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to Ensembl/ensembl-genomio
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Mar 9, 2023
Pending BCBio fix: chapmanb/bcbb#137
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Thanks so much for the fix and apologies for being slow in getting it merged. I'll roll a new release right now as well. Really appreciate you being on top of this. |
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Wonderful thanks a lot for the merge and release @chapmanb! 👍 |
corneliusroemer
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Mar 13, 2023
Biopython was fixed to <=1.80 in #1152 because bcbio-gff <=0.6.9 requires deprecated Biopython functionality that was removed in 1.81 A fix to bcbio-gff was released as 0.7.0, see chapmanb/bcbb#137 chapmanb/bcbb#136 So now we can pin bcbio-gff to >=0.7.0 and remove the pin of Biopython Note added in #1170 can hence be removed
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corneliusroemer
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Biopython was fixed to <=1.80 in #1152 because bcbio-gff <=0.6.9 requires deprecated Biopython functionality that was removed in 1.81 A fix to bcbio-gff was released as 0.7.0, see chapmanb/bcbb#137 chapmanb/bcbb#136 So now we can pin bcbio-gff to >=0.7.0 and remove the pin of Biopython Note added in #1170 can hence be removed
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A possible solution for #136, tested on a minimal sample with python 3.9. Any review/test is welcome to make sure it works in all situations.
With this patch, bcbio-gff should work equally with biopython <=1.80 and biopython 1.81
I know bcbio-gff is not actively maintained anymore, but there's still a ton of code using it, so having a new release with this fix would make life easier