Closed henrikstranneheim closed 10 years ago
Jag har lagt till att http://clinical-db:8082/variants/23548020 returnerar alla compounds som hör till varianten.
Är det du menar?
{
"rating": "",
"location_reliability": "",
"scaled_c_score_snv": 22.8,
"functional_annotation": "nonsynonymous SNV",
"stop_bp": 75490896,
"dbsnp129": null,
"lrt_whole_exome": 2e-06,
"omim_morbid_desc": "",
"rank_score": 27,
"hgnc_synonyms": "",
"phast_const_elements": "Score=668;Name=lod=690",
"snorna_mirna_annotation": "-",
"chr": "chr5",
"hgnc_transcript_id": "SV2C:NM_014979:exon3:c.733C>T:p.L245F,",
"esp6500": null,
"hgnc_symbol": "SV2C",
"GT_call_filter": "PASS",
"pseudogene": "",
"clinical_db_gene_annotation": "NO",
"main_location": "",
"dbsnp132": null,
"disease_group": "",
"ref_nt": "C",
"mutation_taster": 0.991596,
"hgmd_accession": null,
"hgmd": "",
"gene_annotation": "exonic",
"omim_gene_desc": "",
"start_bp": 75490896,
"hgmd_variant_type": null,
"otherVariants": [],
"dbsnp": "-",
"sift_whole_exome": 0.01,
"id": 23548020,
"gerp_element": 909.8,
"dbsnp_id": "-",
"compounds": [
{
"alt_nt": "T",
"start_bp": 75427518,
"chr": "chr5",
"variant": 16159878,
"ref_nt": "C"
},
{
"alt_nt": "A",
"start_bp": 75427935,
"chr": "chr5",
"variant": 16159879,
"ref_nt": "G"
},
{
"alt_nt": "C",
"start_bp": 75470086,
"chr": "chr5",
"variant": 16159880,
"ref_nt": "T"
},
{
"alt_nt": "T",
"start_bp": 75490892,
"chr": "chr5",
"variant": 16159881,
"ref_nt": "C"
}
],
"scaled_c_score_1000g": null,
"hgmd_variant_pmid": null,
"polyphen_var_human": 0.97,
"other_location": "",
"disease_gene_model": null,
"hbvdb": null,
"alt_nt": "T",
"unscaled_c_score_1000g": null,
"phylop_whole_exome": 2.617,
"expression_type": "",
"gene_model": "AR_compound:AD_denovo",
"variant_count": null,
"individual_rank_score": 27,
"unscaled_c_score_snv": 4.33376,
"thousand_g": null,
"ensembl_geneid": "ENSG00000122012;",
"hgnc_approved_name": "synaptic vesicle glycoprotein 2C;",
"genomic_super_dups": "-",
"polyphen_div_human": 0.996,
"gerp_whole_exome": 5.27
}
Precis.
Sen måste MAXcompound scoren ("=XX") för varje variant lyftas ut från strängen och bli globalt sorterbar så att vi kan göra en filtrering på det bästa High scoring compound pair.
"variant": 16159880, är det ett internt ID?
Ja, variant är den interna nyckeln till varianten. Den behövs så att Robin kan göra en länk till varianten.
Jag glömde att ta med combined_score, så här ser compounds entryt ut nu:
"compounds": [
{
"alt_nt": "T",
"ref_nt": "C",
"variant": 16159881,
"combined_score": 42,
"chr": "chr5",
"start_bp": 75490892
},
{
"alt_nt": "A",
"ref_nt": "G",
"variant": 16159879,
"combined_score": 28,
"chr": "chr5",
"start_bp": 75427935
},
{
"alt_nt": "T",
"ref_nt": "C",
"variant": 16159878,
"combined_score": 24,
"chr": "chr5",
"start_bp": 75427518
},
{
"alt_nt": "C",
"ref_nt": "T",
"variant": 16159880,
"combined_score": 24,
"chr": "chr5",
"start_bp": 75470086
}
],
Kanon!
Gör databas parsern grovjobbet med sortering eller gör front-enden det? dvs ska jag engagera Robin?
Databasen levererar compoundsen i en sådan ordning så att den med högst combined_score kommer först.
Nu finns en service som ger alla compounds som tillhör en varint: http://clinical-db.scilifelab.se:8082/compounds/39461415
Som ger:
[
{
"alt_nt": "A",
"ref_nt": "G",
"variant": 37432388,
"combined_score": 25,
"chr": "chr4",
"start_bp": 982852
},
{
"alt_nt": "A",
"ref_nt": "C",
"variant": 37432391,
"combined_score": 25,
"chr": "chr4",
"start_bp": 980896
},
{
"alt_nt": "A",
"ref_nt": "G",
"variant": 37432389,
"combined_score": 24,
"chr": "chr4",
"start_bp": 980932
},
{
"alt_nt": "C",
"ref_nt": "G",
"variant": 37432390,
"combined_score": 21,
"chr": "chr4",
"start_bp": 984870
}
]
chr_start_ref-allel_alt-allel=Compound Score:
for example 17_78184393_C_T=28:17_78187720_A_G=22