diff --git a/src/hub/dataload/sources/dbnsfp/dbnsfp_parser.py b/src/hub/dataload/sources/dbnsfp/dbnsfp_parser.py index 1f1fc669..ea299779 100644 --- a/src/hub/dataload/sources/dbnsfp/dbnsfp_parser.py +++ b/src/hub/dataload/sources/dbnsfp/dbnsfp_parser.py @@ -1,6 +1,5 @@ import re import csv -import glob from enum import Flag from dataclasses import dataclass from itertools import chain @@ -265,10 +264,10 @@ def split_dedup(values: list, sep: str, na_values: set = NA_VALUES): Column("VindijiaNeandertal", dest="vindijia_neandertal", transform=split_genotype), Column("ChagyrskayaNeandertal", dest="chagyrskaya_neandertal", transform=split_genotype), Column("SIFT_score", transform=split_float), - Column("SIFT_converted_rankscore", transform=split_float), + Column("SIFT_converted_rankscore", dest="sift.converted_rankscore", transform=split_float), Column("SIFT_pred", transform=split_str), Column("SIFT4G_score", transform=split_float), - Column("SIFT4G_converted_rankscore", transform=split_float), + Column("SIFT4G_converted_rankscore", dest="sift4g.converted_rankscore", transform=split_float), Column("SIFT4G_pred", transform=split_str), Column("Polyphen2_HDIV_score", transform=split_float), Column("Polyphen2_HDIV_rankscore", transform=split_float), @@ -277,11 +276,11 @@ def split_dedup(values: list, sep: str, na_values: set = NA_VALUES): Column("Polyphen2_HVAR_rankscore", transform=split_float), Column("Polyphen2_HVAR_pred", transform=split_str), Column("LRT_score", transform=split_float), - Column("LRT_converted_rankscore", transform=split_float), + Column("LRT_converted_rankscore", dest="lrt.converted_rankscore", transform=split_float), Column("LRT_pred", transform=split_str), Column("LRT_Omega", transform=split_float), Column("MutationTaster_score", transform=split_float), - Column("MutationTaster_converted_rankscore", transform=split_float), + Column("MutationTaster_converted_rankscore", dest="mutationtaster.converted_rankscore", transform=split_float), Column("MutationTaster_pred", transform=split_str), Column("MutationTaster_model", transform=split_str), Column("MutationTaster_AAE", transform=split_str), @@ -289,10 +288,10 @@ def split_dedup(values: list, sep: str, na_values: set = NA_VALUES): Column("MutationAssessor_rankscore", transform=split_float), Column("MutationAssessor_pred", transform=split_str), Column("FATHMM_score", transform=split_float), - Column("FATHMM_converted_rankscore", transform=split_float), + Column("FATHMM_converted_rankscore", dest="fathmm.converted_rankscore", transform=split_float), Column("FATHMM_pred", transform=split_str), Column("PROVEAN_score", transform=split_float), - Column("PROVEAN_converted_rankscore", transform=split_float), + Column("PROVEAN_converted_rankscore", dest="provean.converted_rankscore", transform=split_float), Column("PROVEAN_pred", transform=split_str), Column("VEST4_score", transform=split_float), Column("VEST4_rankscore", transform=split_float), @@ -340,7 +339,7 @@ def split_dedup(values: list, sep: str, na_values: set = NA_VALUES): Column("LIST-S2_score", transform=split_float), Column("LIST-S2_rankscore", transform=split_float), Column("LIST-S2_pred", transform=split_str), - Column("VARITY_R_score", dest="varity_r.score", transform=split_float), # VARITY new in 4.4.a + Column("VARITY_R_score", dest="varity_r.score", transform=split_float), # new in 4.4.a Column("VARITY_R_rankscore", dest="varity_r.rankscore", transform=split_float), Column("VARITY_ER_score", dest="varity_er.score", transform=split_float), Column("VARITY_ER_rankscore", dest="varity_er.rankscore", transform=split_float), @@ -481,7 +480,7 @@ def split_dedup(values: list, sep: str, na_values: set = NA_VALUES): Column("ExAC_nonpsych_NFE_AF", dest="exac_nonpsych.nfe.af", transform=float), Column("ExAC_nonpsych_SAS_AC", dest="exac_nonpsych.sas.ac", transform=int), Column("ExAC_nonpsych_SAS_AF", dest="exac_nonpsych.sas.af", transform=float), - Column("ALFA_European_AC", dest="alfa.european.ac", transform=int), # new ALFA field, add mapping + Column("ALFA_European_AC", dest="alfa.european.ac", transform=int), Column("ALFA_European_AN", dest="alfa.european.an", transform=int), Column("ALFA_European_AF", dest="alfa.european.af", transform=float), Column("ALFA_African_Others_AC", dest="alfa.african_others.ac", transform=int),