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Error in GFFParser: UnknownSeq is deprecated in biopython 1.81 #136

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Kmassau opened this issue Feb 13, 2023 · 7 comments
Open

Error in GFFParser: UnknownSeq is deprecated in biopython 1.81 #136

Kmassau opened this issue Feb 13, 2023 · 7 comments

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@Kmassau
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Kmassau commented Feb 13, 2023 •
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from Bio.Seq import UnknownSeq is deprecated in biopython 1.81 ( https://github.com/biopython/biopython/blob/dcf52bd4546410e1a60d39fbcd4c0041ec1e6fe6/DEPRECATED.rst#biosequnknownseq) and we have the error below:

    from BCBio.GFF.GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple
/usr/local/lib/python3.9/site-packages/BCBio/GFF/GFFParser.py:34: in <module>
    from Bio.Seq import UnknownSeq
E   ImportError: cannot import name 'UnknownSeq' from 'Bio.Seq' (/usr/local/lib/python3.9/site-packages/Bio/Seq.py)

I am reporting a problem with bcbio-gff-0.6.9, Biopython version 1.81.
@abretaud abretaud mentioned this issue Feb 15, 2023
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@corneliusroemer
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Thanks! This came quite surprising, was there no deprecation warning added in Biopython 1.79? At least that would have allowed us to prepare :/

@corneliusroemer corneliusroemer mentioned this issue Feb 17, 2023
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@abretaud
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no deprecation warning added in Biopython 1.79

I never saw one, but maybe the code is not using it enough to trigger the warning (just an import and isinstance check)

This was referenced Feb 20, 2023
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@victorlin victorlin mentioned this issue Feb 24, 2023
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1 task
@flashlab flashlab mentioned this issue Feb 28, 2023
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@abretaud abretaud mentioned this issue Mar 2, 2023
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bernt-matthias added a commit to bernt-matthias/bioconda-recipes that referenced this issue Mar 2, 2023
@bernt-matthias
bcbio-gff: pin biopython
73b22bc 
xref chapmanb/bcbb#136
@bernt-matthias bernt-matthias mentioned this issue Mar 2, 2023
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BiocondaBot pushed a commit to bioconda/bioconda-recipes that referenced this issue Mar 3, 2023
@bernt-matthias
[ci skip] Merge PR 39703
113d2c2 
Merge PR #39703, commits were: 
 * Apply suggestions from code review
 * bcbio-gff: pin biopython

xref chapmanb/bcbb#136
@abretaud abretaud mentioned this issue Mar 8, 2023
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@StickHu
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StickHu commented Mar 13, 2023

So how can we correct the code to use?

mihailefter added a commit to mutalyzer/retriever that referenced this issue Mar 13, 2023
@mihailefter
Pin biopython version
724deef 
- more details in:
  - mutalyzer/mutalyzer#79
  - chapmanb/bcbb#136
@chapmanb
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Thanks very much for catching this issue and for the fix. There is a new 0.7.0 release on pypi that contains this fix. Apologies again about being slow to get this done and let me know if you run into any issues.

@corneliusroemer
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Excellent, thanks for this @chapmanb! The bioconda recipe needs to unpin Biopython for 0.7.0 then!

@corneliusroemer corneliusroemer mentioned this issue Mar 13, 2023
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corneliusroemer added a commit to nextstrain/augur that referenced this issue Mar 13, 2023
@corneliusroemer
deps: unpin biopython, pin bcbio-gff to 0.7*
928fdcf 
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
@corneliusroemer corneliusroemer mentioned this issue Mar 13, 2023
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corneliusroemer added a commit to nextstrain/augur that referenced this issue Mar 14, 2023
@corneliusroemer
deps: unpin biopython, pin bcbio-gff to 0.7*
7204276 
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
cokelaer pushed a commit to cokelaer/bioconda-recipes that referenced this issue Apr 28, 2023
@bernt-matthias @cokelaer
[ci skip] Merge PR 39703
f1b9b8b 
Merge PR bioconda#39703, commits were: 
 * Apply suggestions from code review
 * bcbio-gff: pin biopython

xref chapmanb/bcbb#136
@victorlin victorlin mentioned this issue Dec 26, 2023
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@victorlin
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was there no deprecation warning added in Biopython 1.79?

There was, but it was suppressed by GFFParser. See #140

@corneliusroemer
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I think this can be closed now as of bcbio-gff 0.7.0

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6 participants
@chapmanb @abretaud @victorlin @corneliusroemer @StickHu @Kmassau