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src/main/resources/example.gz (6402, 2023-09-20)
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src/main/scala/galliaexample/ (0, 2023-09-20)
src/main/scala/galliaexample/dbnsfp/ (0, 2023-09-20)
src/main/scala/galliaexample/dbnsfp/DbNsfp.scala (11095, 2023-09-20)
src/main/scala/galliaexample/dbnsfp/DbNsfpConstants.scala (7085, 2023-09-20)
src/main/scala/galliaexample/dbnsfp/DbNsfpDriver.scala (29615, 2023-09-20)
src/main/scala/galliaexample/dbnsfp/DbNsfpInputFields.scala (40782, 2023-09-20)
src/main/scala/galliaexample/dbnsfp/DbNsfpMutPredTransformer.scala (5698, 2023-09-20)
... ...

For more information, see gallia-core [documentation](https://github.com/galliaproject/gallia-core/blob/init/README.md#introducing-gallia-a-scala-library-for-data-manipulation), in particular the bioinformatics examples [section](https://github.com/galliaproject/gallia-core/blob/init/README.md#bioinformatics-examples). ### Description Test run with: ``` sbt run ``` Uses _Gallia_ [transformations](https://github.com/galliaproject/gallia-dbnsfp/blob/init/src/main/scala/galliaexample/dbnsfp/DbNsfp.scala#L14) to turn TSV rows such as: ```plain #chr pos(1-based) ref alt aaref aaalt rs_dbSNP151 hg19_chr hg19_pos(1-based) hg18_chr hg18_pos(1-based) aapos genename Ensembl_geneid Ensembl_transcriptid Ensembl_proteinid Uniprot_acc Uniprot_entry HGVSc_ANNOVAR HGVSp_ANNOVAR HGVSc_snpEff HGVSp_snpEff HGVSc_VEP HGVSp_VEP APPRIS GENCODE_basic TSL VEP_canonical cds_strand refcodon codonpos codon_degeneracy Ancestral_allele AltaiNeandertal Denisova VindijiaNeandertal SIFT_score SIFT_converted_rankscore SIFT_pred SIFT4G_score SIFT4G_converted_rankscore SIFT4G_pred LRT_score LRT_converted_rankscore LRT_pred LRT_Omega MutationTaster_score MutationTaster_converted_rankscore MutationTaster_pred MutationTaster_model MutationTaster_AAE MutationAssessor_score MutationAssessor_rankscore MutationAssessor_pred FATHMM_score FATHMM_converted_rankscore FATHMM_pred PROVEAN_score PROVEAN_converted_rankscore PROVEAN_pred MetaSVM_score MetaSVM_rankscore MetaSVM_pred MetaLR_score MetaLR_rankscore MetaLR_pred Reliability_index M-CAP_score M-CAP_rankscore M-CAP_pred MutPred_score MutPred_rankscore MutPred_protID MutPred_AAchange MutPred_Top5features MVP_score MVP_rankscore MPC_score MPC_rankscore PrimateAI_score PrimateAI_rankscore PrimateAI_pred DEOGEN2_score DEOGEN2_rankscore DEOGEN2_pred Aloft_Fraction_transcripts_affected Aloft_prob_Tolerant Aloft_prob_Recessive Aloft_prob_Dominant Aloft_pred Aloft_Confidence DANN_score DANN_rankscore fathmm-MKL_coding_score fathmm-MKL_coding_rankscore fathmm-MKL_coding_pred fathmm-MKL_coding_group fathmm-XF_coding_score fathmm-XF_coding_rankscore fathmm-XF_coding_pred Eigen-raw_coding Eigen-raw_coding_rankscore Eigen-pred_coding Eigen-PC-raw_coding Eigen-PC-raw_coding_rankscore Eigen-PC-phred_coding integrated_fitCons_score integrated_fitCons_rankscore integrated_confidence_value GM12878_fitCons_score GM12878_fitCons_rankscore GM12878_confidence_value H1-hESC_fitCons_score H1-hESC_fitCons_rankscore H1-hESC_confidence_value HUVEC_fitCons_score HUVEC_fitCons_rankscore HUVEC_confidence_value GERP++_NR GERP++_RS GERP++_RS_rankscore phyloP100way_vertebrate phyloP100way_vertebrate_rankscore phyloP30way_mammalian phyloP30way_mammalian_rankscore phyloP17way_primate phyloP17way_primate_rankscore phastCons100way_vertebrate phastCons100way_vertebrate_rankscore phastCons30way_mammalian phastCons30way_mammalian_rankscore phastCons17way_primate phastCons17way_primate_rankscore SiPhy_29way_pi SiPhy_29way_logOdds SiPhy_29way_logOdds_rankscore bStatistic bStatistic_rankscore 1000Gp3_AC 1000Gp3_AF 1000Gp3_AFR_AC 1000Gp3_AFR_AF 1000Gp3_EUR_AC 1000Gp3_EUR_AF 1000Gp3_AMR_AC 1000Gp3_AMR_AF 1000Gp3_EAS_AC 1000Gp3_EAS_AF 1000Gp3_SAS_AC 1000Gp3_SAS_AF TWINSUK_AC TWINSUK_AF ALSPAC_AC ALSPAC_AF UK10K_AC UK10K_AF ESP6500_AA_AC ESP6500_AA_AF ESP6500_EA_AC ESP6500_EA_AF ExAC_AC ExAC_AF ExAC_Adj_AC ExAC_Adj_AF ExAC_AFR_AC ExAC_AFR_AF ExAC_AMR_AC ExAC_AMR_AF ExAC_EAS_AC ExAC_EAS_AF ExAC_FIN_AC ExAC_FIN_AF ExAC_NFE_AC ExAC_NFE_AF ExAC_SAS_AC ExAC_SAS_AF ExAC_nonTCGA_AC ExAC_nonTCGA_AF ExAC_nonTCGA_Adj_AC ExAC_nonTCGA_Adj_AF ExAC_nonTCGA_AFR_AC ExAC_nonTCGA_AFR_AF ExAC_nonTCGA_AMR_AC ExAC_nonTCGA_AMR_AF ExAC_nonTCGA_EAS_AC ExAC_nonTCGA_EAS_AF ExAC_nonTCGA_FIN_AC ExAC_nonTCGA_FIN_AF ExAC_nonTCGA_NFE_AC ExAC_nonTCGA_NFE_AF ExAC_nonTCGA_SAS_AC ExAC_nonTCGA_SAS_AF ExAC_nonpsych_AC ExAC_nonpsych_AF ExAC_nonpsych_Adj_AC ExAC_nonpsych_Adj_AF ExAC_nonpsych_AFR_AC ExAC_nonpsych_AFR_AF ExAC_nonpsych_AMR_AC ExAC_nonpsych_AMR_AF ExAC_nonpsych_EAS_AC ExAC_nonpsych_EAS_AF ExAC_nonpsych_FIN_AC ExAC_nonpsych_FIN_AF ExAC_nonpsych_NFE_AC ExAC_nonpsych_NFE_AF ExAC_nonpsych_SAS_AC ExAC_nonpsych_SAS_AF gnomAD_exomes_flag gnomAD_exomes_AC gnomAD_exomes_AN gnomAD_exomes_AF gnomAD_exomes_nhomalt gnomAD_exomes_AFR_AC gnomAD_exomes_AFR_AN gnomAD_exomes_AFR_AF gnomAD_exomes_AFR_nhomalt gnomAD_exomes_AMR_AC gnomAD_exomes_AMR_AN gnomAD_exomes_AMR_AF gnomAD_exomes_AMR_nhomalt gnomAD_exomes_ASJ_AC gnomAD_exomes_ASJ_AN gnomAD_exomes_ASJ_AF gnomAD_exomes_ASJ_nhomalt gnomAD_exomes_EAS_AC gnomAD_exomes_EAS_AN gnomAD_exomes_EAS_AF gnomAD_exomes_EAS_nhomalt gnomAD_exomes_FIN_AC gnomAD_exomes_FIN_AN gnomAD_exomes_FIN_AF gnomAD_exomes_FIN_nhomalt gnomAD_exomes_NFE_AC gnomAD_exomes_NFE_AN gnomAD_exomes_NFE_AF gnomAD_exomes_NFE_nhomalt gnomAD_exomes_SAS_AC gnomAD_exomes_SAS_AN gnomAD_exomes_SAS_AF gnomAD_exomes_SAS_nhomalt gnomAD_exomes_POPMAX_AC gnomAD_exomes_POPMAX_AN gnomAD_exomes_POPMAX_AF gnomAD_exomes_POPMAX_nhomalt gnomAD_exomes_controls_AC gnomAD_exomes_controls_AN gnomAD_exomes_controls_AF gnomAD_exomes_controls_nhomalt gnomAD_exomes_controls_AFR_AC gnomAD_exomes_controls_AFR_AN gnomAD_exomes_controls_AFR_AF gnomAD_exomes_controls_AFR_nhomalt gnomAD_exomes_controls_AMR_AC gnomAD_exomes_controls_AMR_AN gnomAD_exomes_controls_AMR_AF gnomAD_exomes_controls_AMR_nhomalt gnomAD_exomes_controls_ASJ_AC gnomAD_exomes_controls_ASJ_AN gnomAD_exomes_controls_ASJ_AF gnomAD_exomes_controls_ASJ_nhomalt gnomAD_exomes_controls_EAS_AC gnomAD_exomes_controls_EAS_AN gnomAD_exomes_controls_EAS_AF gnomAD_exomes_controls_EAS_nhomalt gnomAD_exomes_controls_FIN_AC gnomAD_exomes_controls_FIN_AN gnomAD_exomes_controls_FIN_AF gnomAD_exomes_controls_FIN_nhomalt gnomAD_exomes_controls_NFE_AC gnomAD_exomes_controls_NFE_AN gnomAD_exomes_controls_NFE_AF gnomAD_exomes_controls_NFE_nhomalt gnomAD_exomes_controls_SAS_AC gnomAD_exomes_controls_SAS_AN gnomAD_exomes_controls_SAS_AF gnomAD_exomes_controls_SAS_nhomalt gnomAD_exomes_controls_POPMAX_AC gnomAD_exomes_controls_POPMAX_AN gnomAD_exomes_controls_POPMAX_AF gnomAD_exomes_controls_POPMAX_nhomalt gnomAD_genomes_flag gnomAD_genomes_AC gnomAD_genomes_AN gnomAD_genomes_AF gnomAD_genomes_nhomalt gnomAD_genomes_AFR_AC gnomAD_genomes_AFR_AN gnomAD_genomes_AFR_AF gnomAD_genomes_AFR_nhomalt gnomAD_genomes_AMR_AC gnomAD_genomes_AMR_AN gnomAD_genomes_AMR_AF gnomAD_genomes_AMR_nhomalt gnomAD_genomes_ASJ_AC gnomAD_genomes_ASJ_AN gnomAD_genomes_ASJ_AF gnomAD_genomes_ASJ_nhomalt gnomAD_genomes_EAS_AC gnomAD_genomes_EAS_AN gnomAD_genomes_EAS_AF gnomAD_genomes_EAS_nhomalt gnomAD_genomes_FIN_AC gnomAD_genomes_FIN_AN gnomAD_genomes_FIN_AF gnomAD_genomes_FIN_nhomalt gnomAD_genomes_NFE_AC gnomAD_genomes_NFE_AN gnomAD_genomes_NFE_AF gnomAD_genomes_NFE_nhomalt gnomAD_genomes_POPMAX_AC gnomAD_genomes_POPMAX_AN gnomAD_genomes_POPMAX_AF gnomAD_genomes_POPMAX_nhomalt gnomAD_genomes_controls_AC gnomAD_genomes_controls_AN gnomAD_genomes_controls_AF gnomAD_genomes_controls_nhomalt gnomAD_genomes_controls_AFR_AC gnomAD_genomes_controls_AFR_AN gnomAD_genomes_controls_AFR_AF gnomAD_genomes_controls_AFR_nhomalt gnomAD_genomes_controls_AMR_AC gnomAD_genomes_controls_AMR_AN gnomAD_genomes_controls_AMR_AF gnomAD_genomes_controls_AMR_nhomalt gnomAD_genomes_controls_ASJ_AC gnomAD_genomes_controls_ASJ_AN gnomAD_genomes_controls_ASJ_AF gnomAD_genomes_controls_ASJ_nhomalt gnomAD_genomes_controls_EAS_AC gnomAD_genomes_controls_EAS_AN gnomAD_genomes_controls_EAS_AF gnomAD_genomes_controls_EAS_nhomalt gnomAD_genomes_controls_FIN_AC gnomAD_genomes_controls_FIN_AN gnomAD_genomes_controls_FIN_AF gnomAD_genomes_controls_FIN_nhomalt gnomAD_genomes_controls_NFE_AC gnomAD_genomes_controls_NFE_AN gnomAD_genomes_controls_NFE_AF gnomAD_genomes_controls_NFE_nhomalt gnomAD_genomes_controls_POPMAX_AC gnomAD_genomes_controls_POPMAX_AN gnomAD_genomes_controls_POPMAX_AF gnomAD_genomes_controls_POPMAX_nhomalt clinvar_id clinvar_clnsig clinvar_trait clinvar_review clinvar_hgvs clinvar_var_source clinvar_MedGen_id clinvar_OMIM_id clinvar_Orphanet_id Interpro_domain GTEx_V7_gene GTEx_V7_tissue Geuvadis_eQTL_target_gene 21 6445558 T A X C . 21 44473990 21 43347059 552;552;552;552;566 CBSL ENSG00000274276;ENSG00000274276;ENSG00000274276;ENSG00000274276;ENSG00000274276 ENST00000624406;ENST00000398168;ENST00000618024;ENST00000617706;ENST00000624934 ENSP00000485669;ENSP00000381234;ENSP00000479559;ENSP00000481719;ENSP00000485527 P0DN79;P0DN79;P0DN79;P0DN79;. CBSL_HUMAN;CBSL_HUMAN;CBSL_HUMAN;CBSL_HUMAN;. c.1656A>T;c.1656A>T;c.1656A>T;c.1656A>T;c.1698A>T p.X552C;p.X552C;p.X552C;p.X552C;p.X566C c.1656A>T;c.1656A>T;c.1656A>T;c.1656A>T;c.1698A>T p.Ter552Cysext*?;p.Ter552Cysext*?;p.Ter552Cysext*?;p.Ter552Cysext*?;p.Ter566Cysext*? c.1656A>T;c.1656A>T;c.1656A>T;c.1656A>T;c.1698A>T p.Ter552CysextTer31;p.Ter552CysextTer31;p.Ter552CysextTer14;p.Ter552CysextTer31;p.Ter566CysextTer31 principal2;principal2;principal2;principal2;alternative2 Y;Y;Y;Y;Y 1;1;1;1;5 .;.;.;YES;. - TGA 3 0 . T/T T/T T/T .;.;.;.;. . .;.;.;.;. .;.;.;.;. . .;.;.;.;. . . . . 1;1;1;1;1;1;1;1;1;1;1;1 0.08975 N;N;N;N;N;N;N;N;N;N;N;N complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae;complex_aae *464C;*566C;*552C;*552C;*552C;*552C;*464C;*552C;*552C;*552C;*552C;*566C .;.;.;.;. . .;.;.;.;. . . . .;.;.;.;. . .;.;.;.;. . . . . . . . . . . . . . . . .;.;.;.;. . .;.;.;.;. . . . . .;.;.;.;. . .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. .;.;.;.;. 0.54113587345593983 0.05073 0.08502 0.14423 N AEFDBHCI . . . 0.200976666004101 0.51248 3.307481 -0.163821194829558 0.32880 1.875051 0.262962 0.04601 0 0.304816 0.05638 0 0.189914 0.04498 0 0.285054 0.05467 0 4.87 2.51 0.29435 0.223000 0.17501 -0.254000 0.08183 0.455000 0.21489 0.000000 0.06391 0.000000 0.01923 0.009000 0.08673 0.0:0.2717:0.0:0.7283 7.5162 0.26770 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .;.;.;.;. . . . ``` into objects like: ```json { "shorthand": "21:44473990;T>A", "locus": { "hg20": { "chromosome": "21", "position": 6445558 }, "hg19": { "chromosome": "21", "position": 44473990 }, "hg18": { "chromosome": "21", "position": 43347059 }, "cds": { "strand": "-" } }, "genes": [ { "AA_position": 552, "symbol": "CBSL", "APPRIS": "principal2", "TSL": "tsl1", "accession": "P0DN79", "codon": { "degeneracy": 0, "ref": "TGA" }, "ensembl": { "gene_id": "ENSG00000274276", "transcript_id": "ENST00000624406", "protein_id": "ENSP00000485669" }, "GENCODE": { "basic": "Y" }, "HGVS": { "c": { "ANNOVAR": "c.1656A>T", "VEP": "c.1656A>T", "snpEff": "c.1656A>T" }, "p": { "ANNOVAR": "p.X552C", "VEP": "p.Ter552CysextTer31", "snpEff": "p.Ter552Cysext*?" } }, "Uniprot": { "entry": "CBSL_HUMAN" } }, { "AA_position": 552, "symbol": "CBSL", "APPRIS": "principal2", "TSL": "tsl1", "accession": "P0DN79", "codon": { "degeneracy": 0, "ref": "TGA" }, "ensembl": { "gene_id": "ENSG00000274276", "transcript_id": "ENST00000398168", "protein_id": "ENSP00000381234" }, "GENCODE": { "basic": "Y" }, "HGVS": { "c": { "ANNOVAR": "c.1656A>T", "VEP": "c.1656A>T", "snpEff": "c.1656A>T" }, "p": { "ANNOVAR": "p.X552C", "VEP": "p.Ter552CysextTer31", "snpEff": "p.Ter552Cysext*?" } }, "Uniprot": { "entry": "CBSL_HUMAN" } }, { "AA_position": 552, "symbol": "CBSL", "APPRIS": "principal2", " ... ...

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