refactor!: remove structural type from variation descriptor #487
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Was not looking at outer coords, but now we are
jsstevenson
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Aug 9, 2023
korikuzma
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Aug 25, 2023
- Refactor app (#474) - Mainly focused on cleanup related to to_vrs and normalize endpoints. Did not really look at gnomad_vcf_to_protein or copy_number_variation modules - Remove to canonical variation (no longer support) - Combined tests for tokenizers/classifiers/validators/translators into one module - Removed amino_acids.csv (accidentally left in) - Names changes - Coding DNA → cDNA - Polypeptide truncation → Protein Stop Gain - Silent Mutation → Reference Agree - Uncertain/Range → Ambiguous - HGVSDupDelModeEnum → HGVSDupDelModeOption - Validators no longer do any kind of translations to VRS representations. Translators will do this work - Classifier only returns exact matches and only returns a single classification rather than a list - Use regex patterns (in variation/regex.py) rather than multiple if/else conditions - Remove unused code - Create variation schemas for supported variation types. Uses consistent field naming - Cleaning up instance variables in classes - Only run fully justified allele normalization on VRS Alleles. Do not run on VRS Copy Number - Pulled tokenize, classify, validate, translate outside of subdirectories (variation/tokenizers, variation/classifiers, variation/validators, variation/translators) and moved to app root - baseline_copies is required in /hgvs_to_copy_number_count - cool-seq-tool update - Removes file path params from QueryHandler, can set these via environment variables - QueryHandler accepts only uta_db_url as param and removes uta_db_pwd - new dependencies for linting - ruff (replaced flake8) - black - Add more support for gnomad vcf expressions in normalize (#479, #489) - Remove pyliftover from deps (covered by cool-seq-tool) (#480) - Fix default mode for hgvs dup del mode wrt rse (#482) - Fix default HGVS dup del mode - dels should be allele w lse (#484) - Use cool-seq-tool AnnotationLayer and rm CoordinateType (#485) - Remove structural type from varaition descriptor (#487)
korikuzma
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Sep 22, 2023
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Close #486