Browser release updates - Githubissues

broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint

BSD 3-Clause "New" or "Revised" License

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Browser release updates #294

Closed ch-kr closed 1 year ago

ch-kr commented 1 year ago

This PR contains code updates required to reformat RMC results for gnomAD browser release.

Major updates: rmc/utils/generic.py

Added two new functions to get reference amino acid information (3 letter code + number) from context HT

rmc/utils/constraint.py

Added functions to annotate RMC results HT with amino acids, then check for and fix any missing amino acid information
Updated reformat_annotations_for_release to reformat RMC HT to new desired schema
Added a function to annotate the globals of the RMC HT for release

Minor changes: rmc/pipeline/regional_constraint.py

Updated code to annotate CDS start and stop positions as transcript start and stops (rather than browser start/stops)
Added call to reformat_annotations_for_release