broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint
BSD 3-Clause "New" or "Revised" License
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PR adding code to create public release (downloadable files) #298

Closed ch-kr closed 1 year ago

ch-kr commented 1 year ago

PR adds code to create three release files:

Note that the current browser release HT exists at this temp path gs://regional_missense_constraint/temp/demo_release.ht with the following schema:

----------------------------------------
Global fields:
    'p_value': float64 
    'all_canonical_transcripts': set<str> 
    'qc_pass_transcripts': set<str> 
    'outlier_transcripts': set<str> 
    'extra_transcripts': set<str> 
    'outlier_transcripts_searched': set<str> 
    'transcripts_searched': set<str> 
    'transcripts_no_rmc_all': set<str> 
    'transcripts_no_rmc_qc': set<str> 
    'rmc_transcripts_all': set<str> 
    'rmc_transcripts_qc': set<str> 
----------------------------------------
Row fields:
    'transcript': str 
    'regions': array<struct {
        start_coordinate: locus<GRCh37>, 
        stop_coordinate: locus<GRCh37>, 
        start_aa: str, 
        stop_aa: str, 
        obs: int64, 
        exp: float64, 
        oe: float64, 
        chisq: float64, 
        p: float64
    }> 
----------------------------------------
Key: ['transcript']

My current plan to run this code is to: