tiny-count: GFF validation and reliability improvements#236

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taimontgomery merged 21 commits intomasterfrom

Oct 16, 2022

Commits on Oct 7, 2022

After further consideration, I've decided to remove the --multi-id option from tiny-count. If multiple ID values are listed, they are now concatenated rather than selecting the first. I think this …
AlexTate
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If a feature lacks an ID/gene_id attribute, but has a Parent attribute, then the value of Parent is used as the ID. It is no longer treated as an error.
AlexTate
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The GFF parsing loop (and error handling) has been moved from ReferenceTables to its own standalone function. This allows parsing machinery to be shared with the new GFFValidation class.
AlexTate
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Unit tests for the new GFFValidation class. Still needs tests for alignment_chroms_mismatch_heuristic()
AlexTate
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Drafted integration of the new GFFValidation class into pipeline startup (configuration.py) and tiny-count startup (counter.py)
AlexTate
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Commits on Oct 9, 2022

Commits on Oct 12, 2022

Commits on Oct 14, 2022

Commits on Oct 15, 2022

Added a test that downloads complete GFF/GTF genomes from Ensemble for C. elegans and Arabidopsis, then runs all four files through ReferenceTables.get(). Genomes need only be downloaded once. Neve…
AlexTate
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