IGVF-DACC / igvf-catalog / d864d1d9-0e0e-403c-a9b9-999121efad4c

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DSERV-785-mutpred2-coding-variants (#440)

* DSERV-785-mutpred2-coding-variants

* close file

* fix bug add sorting by exon number

* splicing site bug fix 1: ref codon fetching

* splicing site bug fix 2: ref pos cal

* add safe guard for normalize part

* add script for parallel running

* add raise error

* add error logs

* add CUG start codon

* return more fields

* fix typo

* type bug

* add ESM mapping

* bug in error message

* adjust esm running

* update return comment

* add protein info to output

* rm del

* add protein to mutpred

* rename adapter

* refactor function for loading enumerated mappings

* add phenotype edge parsing

* add esm adapter separately

* add tests and bug fix

* add more tests to mutpred

* clean old test

* add tests for ESM and bug fix

* use helper for edge _key

* add to data source yaml

* rm files

* fix variation_type

* change one letter code to three letter code

* add function to helper

* fix bug on writing replicate coding variant node

* hgvsc SNV

* add scores to output of mapping files

* adjust mechanism output

* load mutpred phenotype edges from mapping file and fix Met1

* adjust ESM adapter to load phenotype edges from mapping file

* add missing props

* Met1 case for ESM

* bug fix

* fix tests

66 of 129 branches covered (51.16%)

Branch coverage included in aggregate %.

5621 of 15369 relevant lines covered (36.57%)

0.62 hits per line