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Add new dbnsfp 4.6a #184

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merged 21 commits into from
Apr 18, 2024
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85eb4b2
Add new dbnsfp 4.5a
everaldorodrigo Dec 12, 2023
f262209
Merge remote-tracking branch 'origin/master' into new-data-source-format
everaldorodrigo Feb 8, 2024
bef944e
Update number of valid columns.
everaldorodrigo Feb 8, 2024
2d6146e
Add new fields to dbnsfp mapping.
everaldorodrigo Feb 15, 2024
4b971e8
Fix mapping reference for dbnsfp.
everaldorodrigo Feb 15, 2024
6ea5a48
Implement dbnbsfp 4.5a v2.
everaldorodrigo Feb 21, 2024
dcc0ec9
Fix mapping reference for dbnsfp.
everaldorodrigo Feb 22, 2024
fa4f25b
Forces uploading small file for test purpose.
everaldorodrigo Feb 22, 2024
af126ae
Add dbnsfp 4.6a
everaldorodrigo Mar 5, 2024
d24c509
Fix field type on dbnsfp 4.6a v2
everaldorodrigo Mar 5, 2024
661fa2f
Improve dbnsfp parser.
everaldorodrigo Mar 5, 2024
4893f73
In dbnsfp group tissues by gene in the gtex field
everaldorodrigo Mar 8, 2024
d0d25e4
In dbnsfp group tissues by gene in the gtex field
everaldorodrigo Mar 8, 2024
2908c84
Update dbnsfp upload.
everaldorodrigo Mar 13, 2024
ca537dc
Add dbnsfp 4.7a
everaldorodrigo Mar 13, 2024
92a8858
Add comment to clingen datasource no longer maintained.
everaldorodrigo Mar 14, 2024
5e691ac
Update dbnsfp v1 mapping to 4.7a
everaldorodrigo Mar 14, 2024
a75e063
Update dbnsfp v1 mapping to 4.7a: fix errors
everaldorodrigo Mar 15, 2024
9835323
Update dbnsfp v2 mapping to 4.7a
everaldorodrigo Mar 15, 2024
7bc0d57
Fix mapping type for dbnsfp.
everaldorodrigo Mar 19, 2024
20e18c5
Fix dbnsfp index mapping.
everaldorodrigo Mar 25, 2024
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Fix field type on dbnsfp 4.6a v2
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everaldorodrigo committed Mar 5, 2024
commit d24c509b173d29d4b0aef48bc2b6b7bb3082c5ea
4 changes: 2 additions & 2 deletions src/hub/dataload/sources/dbnsfp/dbnsfp_parser_46a_v2.py
Original file line number Diff line number Diff line change
Expand Up @@ -371,10 +371,10 @@ def split_zip(values: list[str], sep: str, na_values: set = NA_VALUES):
Column("VARITY_R_LOO_rankscore", dest="varity.r_loo.rankscore", transform=split_float_drop_na),
Column("VARITY_ER_LOO_score", dest="varity.er_loo.score", transform=split_float_drop_na),
Column("VARITY_ER_LOO_rankscore", dest="varity.er_loo.rankscore", transform=split_float_drop_na),
Column("ESM1b_score", dest="esm1b.score", transform=split_float), # new in 4.5.a
Column("ESM1b_score", dest="esm1b.score", transform=split_float_drop_na), # new in 4.5.a
Column("ESM1b_rankscore", dest="esm1b.rankscore", transform=split_float_drop_na), # new in 4.5.a
Column("ESM1b_pred", dest="esm1b.pred", transform=split_str_drop_na), # new in 4.5.a
Column("EVE_score", dest="eve.score", transform=split_float), # new in 4.5.a
Column("EVE_score", dest="eve.score", transform=split_float_drop_na), # new in 4.5.a
Column("EVE_rankscore", dest="eve.rankscore", transform=split_float_drop_na), # new in 4.5.a
Column("EVE_Class10_pred", dest="eve.class10_pred", transform=split_str_drop_na), # new in 4.5.a
Column("EVE_Class20_pred", dest="eve.class20_pred", transform=split_str_drop_na), # new in 4.5.a
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