Fix translate #1109
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Fix translate #1109
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…re type source for vcf and alignment mode. Fixes nextstrain#1108 by moving the warning about padding outside of translate_vcf_feature where the feature name is also available and does not need to be passed on to translate_vcf_feature
jameshadfield
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Dec 4, 2023
This check is already in place for non-VCF inputs, and my guess is it was omitted here as the TB pipeline's GFF file didn't include a 'source' annotation. I don't think 'source' is actually a valid GFF ID and I suspect we've just been applying the INSDC/GenBank term to GFF files, but it is one of the two fields parsed by `load_features` and there are GFF files in Nextstrain build pipelines which use it. Modifying the underlying `load_features` would be a better solution, but that's a bigger project for another day. We additionally update the error message to use the same feature name we export. Closes #591 Supersedes #1109
jameshadfield
added a commit
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this pull request
Dec 4, 2023
This check is already in place for non-VCF inputs, and my guess is it was omitted here as the TB pipeline's GFF file didn't include a 'source' annotation. I don't think 'source' is actually a valid GFF ID and I suspect we've just been applying the INSDC/GenBank term to GFF files, but it is one of the two fields parsed by `load_features` and there are GFF files in Nextstrain build pipelines which use it. Modifying the underlying `load_features` would be a better solution, but that's a bigger project for another day. We additionally update the error message to use the same feature name we export. Closes #591 Supersedes #1109
jameshadfield
added a commit
that referenced
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Dec 5, 2023
This check is already in place for non-VCF inputs, and my guess is it was omitted here as the TB pipeline's GFF file didn't include a 'source' annotation. I don't think 'source' is actually a valid GFF ID and I suspect we've just been applying the INSDC/GenBank term to GFF files, but it is one of the two fields parsed by `load_features` and there are GFF files in Nextstrain build pipelines which use it. Modifying the underlying `load_features` would be a better solution, but that's a bigger project for another day. We additionally update the error message to use the same feature name we export. Closes #591 Supersedes #1109
jameshadfield
added a commit
that referenced
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Dec 11, 2023
This check is already in place for non-VCF inputs, and my guess is it was omitted here as the TB pipeline's GFF file didn't include a 'source' annotation. I don't think 'source' is actually a valid GFF ID and I suspect we've just been applying the INSDC/GenBank term to GFF files, but it is one of the two fields parsed by `load_features` and there are GFF files in Nextstrain build pipelines which use it. Modifying the underlying `load_features` would be a better solution, but that's a bigger project for another day. We additionally update the error message to use the same feature name we export. Closes #591 Supersedes #1109
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Thanks for this @andreott, and sorry it slipped through the cracks for so long. The underlying issue has been addressed by #1348. Please see comment #1348 (comment) for more details. |
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Description of proposed changes
Fixes #591 in translate.py by perfoming the check for feature type source for vcf and alignment mode.
Fixes #1108 by moving the warning about padding outside of translate_vcf_feature where the feature name is also available and does not need to be passed on to translate_vcf_feature
Related issue(s)
Fixes #591
Fixes #1108
Testing
What steps should be taken to test the changes you've proposed?
If you added or changed behavior in the codebase, did you update the tests, or do you need help with this?
I ran it on my vcd input data and it worked. Should not effect any other code parts
Checklist