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Merge pull request #102 from biothings/dbNSFP_v4.1
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Update dbNSFP parser and uploader to work with new v4.1 dbNSFP release
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@kevinxin90
kevinxin90 committed Aug 6, 2020
2 parents ee4ee75 + e45c7da commit 3df4e56
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Showing 2 changed files with 58 additions and 39 deletions.
69 changes: 30 additions & 39 deletions src/hub/dataload/sources/dbnsfp/dbnsfp_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
from biothings.utils.dataload import list_split, dict_sweep, unlist, value_convert_to_number
from biothings.utils.common import anyfile

VALID_COLUMN_NO = 376
VALID_COLUMN_NO = 367

'''this parser is for dbNSFP v3.5a beta2 downloaded from
'''this parser is for dbNSFP v4.1a downloaded from
https://sites.google.com/site/jpopgen/dbNSFP'''

# convert one snp to json
Expand Down Expand Up @@ -41,8 +41,8 @@ def _map_line_to_json(df, version, include_gnomad, index=0):
else:
freq = siphy_29way_pi.split(":")
siphy = {'a': freq[0], 'c': freq[1], 'g': freq[2], 't': freq[3]}
gtex_gene = df["GTEx_V7_gene"].split('|')
gtex_tissue = df["GTEx_V7_tissue"].split('|')
gtex_gene = df["GTEx_V8_gene"].split('|')
gtex_tissue = df["GTEx_V8_tissue"].split('|')
gtex = map(dict, map(lambda t: zip(('gene', 'tissue'), t), zip(gtex_gene, gtex_tissue)))
acc = df["Uniprot_acc"].rstrip().rstrip(';').split(";")
entry = df["Uniprot_entry"].rstrip().rstrip(';').split(";")
Expand Down Expand Up @@ -202,6 +202,10 @@ def norm(arr):
"afr_af": df["gnomAD_genomes_AFR_AF"],
"afr_an": df["gnomAD_genomes_AFR_AN"],
"afr_nhomalt": df["gnomAD_genomes_AFR_nhomalt"],
"ami_ac": df["gnomAD_genomes_AMI_AC"],
"ami_an": df["gnomAD_genomes_AMI_AN"],
"ami_af": df["gnomAD_genomes_AMI_AF"],
"ami_nhomalt": df["gnomAD_genomes_AMI_nhomalt"],
"amr_ac": df["gnomAD_genomes_AMR_AC"],
"amr_an": df["gnomAD_genomes_AMR_AN"],
"amr_af": df["gnomAD_genomes_AMR_AF"],
Expand All @@ -226,41 +230,6 @@ def norm(arr):
"popmax_af": df["gnomAD_genomes_POPMAX_AF"],
"popmax_an": df["gnomAD_genomes_POPMAX_AN"],
"popmax_nhomalt": df["gnomAD_genomes_POPMAX_nhomalt"]
},
"gnomad_genomes_controls": {
"nhomalt": df["gnomAD_genomes_controls_nhomalt"],
"ac": df["gnomAD_genomes_controls_AC"],
"an": df["gnomAD_genomes_controls_AN"],
"af": df["gnomAD_genomes_controls_AF"],
"nhomalt": df["gnomAD_genomes_controls_nhomalt"],
"afr_ac": df["gnomAD_genomes_controls_AFR_AC"],
"afr_af": df["gnomAD_genomes_controls_AFR_AF"],
"afr_an": df["gnomAD_genomes_controls_AFR_AN"],
"afr_nhomalt": df["gnomAD_genomes_controls_AFR_nhomalt"],
"amr_ac": df["gnomAD_genomes_controls_AMR_AC"],
"amr_an": df["gnomAD_genomes_controls_AMR_AN"],
"amr_af": df["gnomAD_genomes_controls_AMR_AF"],
"amr_nhomalt": df["gnomAD_genomes_controls_AMR_nhomalt"],
"asj_ac": df["gnomAD_genomes_controls_ASJ_AC"],
"asj_an": df["gnomAD_genomes_controls_ASJ_AN"],
"asj_af": df["gnomAD_genomes_controls_ASJ_AF"],
"asj_nhomalt": df["gnomAD_genomes_controls_ASJ_nhomalt"],
"eas_ac": df["gnomAD_genomes_controls_EAS_AC"],
"eas_af": df["gnomAD_genomes_controls_EAS_AF"],
"eas_an": df["gnomAD_genomes_controls_EAS_AN"],
"eas_nhomalt": df["gnomAD_genomes_controls_EAS_nhomalt"],
"fin_ac": df["gnomAD_genomes_controls_FIN_AC"],
"fin_af": df["gnomAD_genomes_controls_FIN_AF"],
"fin_an": df["gnomAD_genomes_controls_FIN_AN"],
"fin_nhomalt": df["gnomAD_genomes_controls_FIN_nhomalt"],
"nfe_ac": df["gnomAD_genomes_controls_NFE_AC"],
"nfe_af": df["gnomAD_genomes_controls_NFE_AF"],
"nfe_an": df["gnomAD_genomes_controls_NFE_AN"],
"nfe_nhomalt": df["gnomAD_genomes_controls_NFE_nhomalt"],
"popmax_ac": df["gnomAD_genomes_controls_POPMAX_AC"],
"popmax_af": df["gnomAD_genomes_controls_POPMAX_AF"],
"popmax_an": df["gnomAD_genomes_controls_POPMAX_AN"],
"popmax_nhomalt": df["gnomAD_genomes_controls_POPMAX_nhomalt"]
}
}

Expand Down Expand Up @@ -508,6 +477,28 @@ def norm(arr):
"logodds": df["SiPhy_29way_logOdds"],
"logodds_rankscore": df["SiPhy_29way_logOdds_rankscore"]
},
"bayesdel": {
"add_af": {
"score": df["BayesDel_addAF_score"],
"rankscore": df["BayesDel_addAF_rankscore"],
"pred": df["BayesDel_addAF_pred"]
},
"no_af": {
"score": df["BayesDel_noAF_score"],
"rankscore": df["BayesDel_noAF_rankscore"],
"pred": df["BayesDel_noAF_pred"]
}
},
"clinpred": {
"score": df["ClinPred_score"],
"rankscore": df["ClinPred_rankscore"],
"pred": df["ClinPred_pred"]
},
"list-s2": {
"score": df["LIST-S2_score"],
"rankscore": df["LIST-S2_rankscore"],
"pred": df["LIST-S2_pred"]
},
"1000gp3": {
"ac": df["1000Gp3_AC"],
"af": df["1000Gp3_AF"],
Expand Down
28 changes: 28 additions & 0 deletions src/hub/dataload/sources/dbnsfp/dbnsfp_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -681,6 +681,34 @@ def get_mapping(klass):
}
}
},
"clinpred": {
"properties": {
"score": {
"type": "float"
},
"rankscore": {
"type": "float"
},
"pred": {
"type": "keyword",
"normalizer": "keyword_lowercase_normalizer"
}
}
},
"list-s2s": {
"properties": {
"score": {
"type": "float"
},
"rankscore": {
"type": "float"
},
"pred": {
"type": "keyword",
"normalizer": "keyword_lowercase_normalizer"
}
}
},
"metalr": {
"properties": {
"score": {
Expand Down

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