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broadinstitute / regional_missense_constraint

Code to calculate regional missense constraint
BSD 3-Clause "New" or "Revised" License
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Update requirements.txt #271

Closed illusional closed 1 year ago

illusional commented 1 year ago

From general poking around the code.

Unaddressed:

I suspect some of these may not be completely correct due to the pylint warning:

************* Module rmc.utils.generic
rmc/utils/generic.py:9:0: E0611: No name 'annotate_exploded_vep_for_constraint_groupings' in module 'gnomad.utils.constraint' (no-name-in-module)
rmc/utils/generic.py:21:0: E0401: Unable to import 'gnomad_constraint.utils.constraint' (import-error)
rmc/utils/generic.py:388:26: E1123: Unexpected keyword argument 'trimers' in function call (unexpected-keyword-arg)
rmc/utils/generic.py:391:26: E1123: Unexpected keyword argument 'trimers' in function call (unexpected-keyword-arg)
rmc/utils/generic.py:563:4: E0401: Unable to import 'reference_data.de_novo_tsv' (import-error)
rmc/utils/generic.py:564:4: E0401: Unable to import 'reference_data.de_novo.path' (import-error)
************* Module rmc.utils.mpc
rmc/utils/mpc.py:4:0: E0611: No name 'dmatrices' in module 'patsy' (no-name-in-module)

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