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Is it possible to import my own cds fasta file for annotation? #245

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PengfanZhang opened this issue Oct 2, 2023 · 3 comments
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Is it possible to import my own cds fasta file for annotation? #245

PengfanZhang opened this issue Oct 2, 2023 · 3 comments
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feature
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v1.9.0

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@PengfanZhang
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Hi, I have my own cds file predicted from prodigal with customized translation table. I'm wondering if bakta offers the option to annotate user-specified cds files rather than starting from scratch?
@PengfanZhang PengfanZhang added the enhancement New feature or request label Oct 2, 2023
@oschwengers
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Hi @PengfanZhang , thanks for asking. Unfortunately, this is currently not possible. As this is asked for more and more often, we might consider implementing this - however, we cannot provide any reasonable ETA.

@simone-pignotti simone-pignotti mentioned this issue Oct 9, 2023
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@oschwengers oschwengers mentioned this issue Oct 24, 2023
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@oschwengers
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Ok, since more and more users ask for a feature like this, I've started a new issue #250 collecting ideas and requirements. Feedback and input is highly welcome!

@oschwengers oschwengers added feature and removed enhancement New feature or request labels Oct 24, 2023
@oschwengers oschwengers added this to the v1.9.0 milestone Nov 27, 2023
@oschwengers
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OK, with #250 I'd consider this as addressed. You can now provide CDS coordindates as GFF/Genbank via --regions and if required or desired, in addition, provide accompanying functional information via --proteins.

Just in case there are any questions or unaddressed use cases, please, do not hesitate to re-open this or another issue.

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