From a9ac6739a0e7aa0fc9813fb3624d88a8fa3b96b2 Mon Sep 17 00:00:00 2001 From: Anja Thormann <anja@ebi.ac.uk> Date: Fri, 12 Feb 2016 17:14:48 +0000 Subject: [PATCH] new human variation test database --- .../homo_sapiens/variation/allele.txt | 1 + .../homo_sapiens/variation/allele_code.txt | 0 .../variation/associate_study.txt | 0 .../homo_sapiens/variation/attrib.txt | 337 ++++++++++++++++++ .../homo_sapiens/variation/attrib_set.txt | 247 +++++++++++++ .../homo_sapiens/variation/attrib_type.txt | 33 ++ .../variation/compressed_genotype_region.txt | 0 .../variation/compressed_genotype_var.txt | 0 .../homo_sapiens/variation/coord_system.txt | 0 .../homo_sapiens/variation/display_group.txt | 0 .../homo_sapiens/variation/failed_allele.txt | 0 .../variation/failed_description.txt | 19 + .../variation/failed_structural_variation.txt | 0 .../variation/failed_variation.txt | 0 .../homo_sapiens/variation/genotype_code.txt | 0 .../homo_sapiens/variation/individual.txt | 0 .../variation/individual_synonym.txt | 0 .../variation/individual_type.txt | 4 + .../homo_sapiens/variation/meta.txt | 3 + .../homo_sapiens/variation/meta_coord.txt | 3 + .../variation/motif_feature_variation.txt | 0 .../homo_sapiens/variation/phenotype.txt | 2 + .../variation/phenotype_feature.txt | 2 + .../variation/phenotype_feature_attrib.txt | 0 .../homo_sapiens/variation/population.txt | 1 + .../variation/population_genotype.txt | 0 .../variation/population_structure.txt | 0 .../variation/population_synonym.txt | 0 .../protein_function_predictions.txt | 0 .../protein_function_predictions_attrib.txt | 0 .../homo_sapiens/variation/publication.txt | 0 .../homo_sapiens/variation/read_coverage.txt | 0 .../regulatory_feature_variation.txt | 0 .../homo_sapiens/variation/sample.txt | 0 .../variation/sample_genotype_multiple_bp.txt | 0 .../variation/sample_population.txt | 0 .../homo_sapiens/variation/seq_region.txt | 1 + .../homo_sapiens/variation/source.txt | 1 + .../variation/strain_gtype_poly.txt | 0 .../variation/structural_variation.txt | 3 + .../structural_variation_association.txt | 0 .../structural_variation_feature.txt | 3 + .../variation/structural_variation_sample.txt | 0 .../homo_sapiens/variation/study.txt | 1 + .../variation/submitter_handle.txt | 0 .../homo_sapiens/variation/subsnp_handle.txt | 0 .../variation/tagged_variation_feature.txt | 0 .../tmp_sample_genotype_single_bp.txt | 0 .../variation/transcript_variation.txt | 0 .../variation/translation_md5.txt | 0 .../homo_sapiens/variation/variation.txt | 3 + .../variation/variation_attrib.txt | 0 .../variation/variation_citation.txt | 0 .../variation/variation_feature.txt | 3 + .../variation/variation_genename.txt | 0 .../homo_sapiens/variation/variation_hgvs.txt | 0 .../homo_sapiens/variation/variation_set.txt | 1 + .../variation_set_structural_variation.txt | 2 + .../variation/variation_set_structure.txt | 0 .../variation/variation_set_variation.txt | 2 + .../variation/variation_synonym.txt | 0 61 files changed, 672 insertions(+) create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/allele.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/allele_code.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/associate_study.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/attrib.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/attrib_set.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/attrib_type.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/compressed_genotype_region.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/compressed_genotype_var.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/coord_system.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/display_group.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/failed_allele.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/failed_structural_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/failed_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/genotype_code.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/individual.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/individual_synonym.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/individual_type.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/meta_coord.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/motif_feature_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature_attrib.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/population.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/population_genotype.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/population_structure.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/population_synonym.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/protein_function_predictions.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/protein_function_predictions_attrib.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/publication.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/read_coverage.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/regulatory_feature_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/sample.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/sample_genotype_multiple_bp.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/sample_population.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/seq_region.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/source.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/strain_gtype_poly.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_association.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_sample.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/study.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/submitter_handle.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/subsnp_handle.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/tagged_variation_feature.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/tmp_sample_genotype_single_bp.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/transcript_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/translation_md5.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_attrib.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_citation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_feature.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_genename.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_hgvs.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_set.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structural_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structure.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_variation.txt create mode 100644 modules/t/test-genome-DBs/homo_sapiens/variation/variation_synonym.txt diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/allele.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/allele.txt new file mode 100644 index 0000000000..b662e7a1f9 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/allele.txt @@ -0,0 +1 @@ +1 1 \N 0 1 0.8 \N \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/allele_code.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/allele_code.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/associate_study.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/associate_study.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/attrib.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/attrib.txt new file mode 100644 index 0000000000..06d6ff2926 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/attrib.txt @@ -0,0 +1,337 @@ +2 2 SNV +1 1 SO:0001483 +3 3 SNP +5 2 substitution +4 1 SO:1000002 +7 2 copy_number_variation +6 1 SO:0001019 +8 3 CNV +10 2 insertion +9 1 SO:0000667 +12 2 deletion +11 1 SO:0000159 +14 2 indel +13 1 SO:1000032 +16 2 tandem_repeat +15 1 SO:0000705 +18 2 sequence_alteration +17 1 SO:0001059 +375 2 genetic_marker +376 1 SO:0001645 +111 2 structural_variant +112 1 SO:0001537 +113 3 SV +114 2 probe +115 1 SO:0000051 +116 3 CNV_PROBE +200 2 copy_number_gain +201 1 SO:0001742 +202 3 Gain +203 2 copy_number_loss +204 1 SO:0001743 +205 3 Loss +206 2 inversion +207 1 SO:1000036 +208 2 complex_structural_alteration +209 1 SO:0001784 +210 3 Complex +211 2 tandem_duplication +212 1 SO:1000173 +213 3 Tandem duplication +242 2 mobile_element_insertion +243 1 SO:0001837 +244 3 Mobile element insertion +286 2 interchromosomal_breakpoint +287 1 SO:0001873 +288 3 Interchromosomal breakpoint +289 2 intrachromosomal_breakpoint +290 1 SO:0001874 +291 3 Intrachromosomal breakpoint +292 2 translocation +293 1 SO:0000199 +253 2 duplication +254 1 SO:1000035 +331 3 Duplication +361 2 novel_sequence_insertion +362 1 SO:0001838 +363 3 Novel sequence insertion +19 1 SO:0001628 +20 2 intergenic_variant +294 6 38 +21 3 INTERGENIC +118 5 transcript +295 1 SO:0001631 +296 2 upstream_gene_variant +266 6 24 +24 3 UPSTREAM +297 1 SO:0001632 +298 2 downstream_gene_variant +265 6 25 +27 3 DOWNSTREAM +125 4 splice-5 +126 5 primary_transcript +32 1 SO:0001575 +33 2 splice_donor_variant +145 6 3 +34 3 ESSENTIAL_SPLICE_SITE +128 4 splice-3 +129 1 SO:0001574 +36 2 splice_acceptor_variant +37 1 SO:0001630 +38 2 splice_region_variant +135 6 13 +39 3 SPLICE_SITE +131 4 intron +40 1 SO:0001627 +41 2 intron_variant +120 6 21 +42 3 INTRONIC +133 4 untranslated_5 +134 5 mRNA +43 1 SO:0001623 +44 2 5_prime_UTR_variant +122 6 18 +45 3 5PRIME_UTR +136 4 untranslated_3 +46 1 SO:0001624 +47 2 3_prime_UTR_variant +124 6 19 +48 3 3PRIME_UTR +139 4 cds-synon +299 1 SO:0001819 +300 2 synonymous_variant +132 6 15 +54 3 SYNONYMOUS_CODING +141 4 missense +55 1 SO:0001583 +301 2 missense_variant +153 6 12 +57 3 NON_SYNONYMOUS_CODING +302 1 SO:0001821 +303 2 inframe_insertion +140 6 10 +304 1 SO:0001822 +305 2 inframe_deletion +154 6 11 +144 4 nonsense +62 1 SO:0001587 +63 2 stop_gained +146 6 4 +64 3 STOP_GAINED +65 1 SO:0001578 +66 2 stop_lost +143 6 6 +67 3 STOP_LOST +68 1 SO:0001567 +69 2 stop_retained_variant +70 1 SO:0002012 +306 2 start_lost +142 6 7 +147 4 frameshift +72 1 SO:0001589 +73 2 frameshift_variant +138 6 5 +74 3 FRAMESHIFT_CODING +75 1 SO:0001626 +76 2 incomplete_terminal_codon_variant +137 6 14 +77 3 PARTIAL_CODON +78 1 SO:0001621 +79 2 NMD_transcript_variant +262 6 22 +80 3 NMD_TRANSCRIPT +150 5 ncRNA +81 1 SO:0001619 +82 2 non_coding_transcript_variant +263 6 23 +83 3 WITHIN_NON_CODING_GENE +307 1 SO:0001792 +308 2 non_coding_transcript_exon_variant +119 6 20 +152 5 miRNA +84 1 SO:0001620 +85 2 mature_miRNA_variant +151 6 17 +86 3 WITHIN_MATURE_miRNA +87 1 SO:0001580 +88 2 coding_sequence_variant +149 6 16 +89 3 CODING_UNKNOWN +155 5 regulatory_region +90 1 SO:0001566 +91 2 regulatory_region_variant +309 6 36 +92 3 REGULATORY_REGION +157 5 TF_binding_site +158 1 SO:0001782 +159 2 TF_binding_site_variant +310 6 30 +311 1 SO:0001893 +312 2 transcript_ablation +127 6 1 +313 1 SO:0001889 +314 2 transcript_amplification +130 6 8 +315 1 SO:0001895 +316 2 TFBS_ablation +261 6 26 +317 1 SO:0001892 +318 2 TFBS_amplification +319 6 28 +320 1 SO:0001894 +321 2 regulatory_region_ablation +322 6 31 +323 1 SO:0001891 +324 2 regulatory_region_amplification +325 6 33 +346 5 sequence_feature +326 1 SO:0001907 +327 2 feature_elongation +328 1 SO:0001906 +329 2 feature_truncation +330 6 37 +416 1 SO:0001818 +417 2 protein_altering_variant +98 2 mRNA +97 1 SO:0000234 +100 2 transcript +99 1 SO:0000673 +102 2 primary_transcript +101 1 SO:0000185 +104 2 ncRNA +103 1 SO:0000655 +106 2 miRNA +105 1 SO:0000276 +108 2 regulatory_region +107 1 SO:0005836 +110 2 binding_site +109 1 SO:0000409 +255 2 sequence_feature +256 1 SO:0000110 +377 420 uncertain significance +378 420 not provided +379 420 benign +380 420 likely benign +381 420 likely pathogenic +382 420 pathogenic +383 420 drug response +384 420 histocompatibility +385 420 other +386 420 confers sensitivity +387 420 risk factor +388 420 association +389 420 protective +215 10 unknown +216 10 untested +217 10 non-pathogenic +218 10 probable-non-pathogenic +219 10 probable-pathogenic +220 10 pathogenic +221 10 drug-response +222 10 histocompatibility +223 10 other +176 9 hapmap +177 9 ind_venter +178 9 ind_watson +179 9 fail_all +180 9 fail_nonref +181 9 fail_ambig +182 9 fail_gt_fq +183 9 fail_incons_map +184 9 fail_mult_map +185 9 fail_no_alleles +186 9 fail_no_gt +187 9 fail_no_map +188 9 fail_no_seq +189 9 fail_non_nt +190 9 fail_mult_alleles +214 9 fail_dbsnp_suspect +191 9 ph_hgmd_pub +193 9 ph_nhgri +194 9 ph_omim +195 9 ph_variants +196 9 ph_uniprot +197 9 ph_cosmic +198 9 ph_ega +257 9 hapmap_ceu +258 9 hapmap_hcb +259 9 hapmap_jpt +260 9 hapmap_yri +332 9 Affy_500K +333 9 Affy_SNP6 +337 9 Cardio-Metabo_Chip +338 9 HumanOmni1-Quad +335 9 Illumina_1M-duo +334 9 Illumina_660Q +339 9 Illumina_CytoSNP12v1 +342 9 Human610_Quad +343 9 HumanHap550 +340 9 HumanHap650Y +341 9 HumanOmni2.5 +245 9 PorcineSNP60 +344 9 esp_6500 +345 9 clin_assoc +360 9 all_chips +348 9 Chicken600K +349 9 EquineSNP50 +350 9 BovineHD +351 9 BovineLD +352 9 BovineSNP50 +355 9 phencode +354 9 HumanOmni5 +356 9 OvineSNP50 +357 9 OvineHDSNP +358 9 ExomeChip +359 9 ImmunoChip +373 9 HumanOmniExpress +374 9 ClinVar +353 9 MGP +390 9 HumanCoreExome +404 9 1kg_3 +405 9 1kg_3_afr +406 9 1kg_3_amr +407 9 1kg_3_eas +408 9 1kg_3_sas +409 9 1kg_3_eur +410 9 1kg_3_com +411 9 1kg_3_afr_com +412 9 1kg_3_amr_com +413 9 1kg_3_eas_com +414 9 1kg_3_sas_com +415 9 1kg_3_eur_com +395 9 LSDB +396 9 dbPEX +397 9 HbVar +398 9 Infevers +399 9 KAT6BDB +400 9 LMDD +401 9 OIVD +402 9 PAHdb +270 8 tolerated +271 8 deleterious +391 8 tolerated - low confidence +392 8 deleterious - low confidence +272 7 probably damaging +273 7 possibly damaging +274 7 benign +275 7 unknown +267 12 sift +268 12 polyphen_humvar +269 12 polyphen_humdiv +224 11 Not tested +225 11 Benign +226 11 Pathogenic +227 11 Uncertain Significance +228 11 likely benign +229 11 likely pathogenic +364 11 not provided +365 11 association +366 11 risk factor +367 419 Multiple_observations +368 419 Frequency +369 419 HapMap +370 419 1000Genomes +371 419 Cited +372 419 ESP +418 419 Phenotype_or_Disease +421 419 ExAC diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/attrib_set.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/attrib_set.txt new file mode 100644 index 0000000000..b36010e2e2 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/attrib_set.txt @@ -0,0 +1,247 @@ +1 1 +1 2 +1 3 +2 4 +2 5 +3 6 +3 7 +3 8 +4 9 +4 10 +5 11 +5 12 +6 13 +6 14 +7 15 +7 16 +8 17 +8 18 +38 97 +38 98 +39 99 +39 100 +40 101 +40 102 +41 103 +41 104 +42 105 +42 106 +43 107 +43 108 +44 109 +44 110 +45 111 +45 112 +45 113 +46 114 +46 115 +46 116 +49 200 +49 201 +49 202 +50 203 +50 204 +50 205 +51 206 +51 207 +52 208 +52 209 +52 210 +53 211 +53 212 +53 213 +54 242 +54 243 +54 244 +60 255 +60 256 +79 72 +79 73 +79 74 +79 134 +79 138 +79 147 +87 286 +87 287 +87 288 +88 289 +88 290 +88 291 +89 292 +89 293 +90 19 +90 20 +90 21 +90 294 +91 24 +91 118 +91 266 +91 295 +91 296 +92 27 +92 118 +92 265 +92 297 +92 298 +93 32 +93 33 +93 34 +93 125 +93 126 +93 145 +94 34 +94 36 +94 126 +94 128 +94 129 +94 145 +95 37 +95 38 +95 39 +95 126 +95 135 +97 43 +97 44 +97 45 +97 122 +97 133 +97 134 +98 46 +98 47 +98 48 +98 124 +98 134 +98 136 +99 54 +99 132 +99 134 +99 139 +99 299 +99 300 +100 55 +100 57 +100 134 +100 141 +100 153 +100 301 +101 57 +101 134 +101 140 +101 302 +101 303 +102 57 +102 134 +102 154 +102 304 +102 305 +103 62 +103 63 +103 64 +103 134 +103 144 +103 146 +104 65 +104 66 +104 67 +104 134 +104 143 +105 54 +105 68 +105 69 +105 132 +105 134 +106 57 +106 70 +106 134 +106 142 +106 306 +107 75 +107 76 +107 77 +107 134 +107 137 +109 81 +109 82 +109 83 +109 150 +109 263 +111 84 +111 85 +111 86 +111 151 +111 152 +112 87 +112 88 +112 89 +112 134 +112 149 +113 90 +113 91 +113 92 +113 155 +113 309 +114 92 +114 157 +114 158 +114 159 +114 310 +115 127 +115 134 +115 311 +115 312 +116 130 +116 134 +116 313 +116 314 +117 157 +117 261 +117 315 +117 316 +118 157 +118 317 +118 318 +118 319 +119 157 +119 320 +119 321 +119 322 +120 157 +120 323 +120 324 +120 325 +121 309 +121 326 +121 327 +121 346 +122 328 +122 329 +122 330 +122 346 +123 253 +123 254 +123 331 +124 40 +124 41 +124 42 +124 120 +124 126 +124 131 +125 78 +125 79 +125 80 +125 134 +125 262 +126 83 +126 119 +126 150 +126 307 +126 308 +127 361 +127 362 +127 363 +128 375 +128 376 +129 134 +129 153 +129 416 +129 417 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/attrib_type.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/attrib_type.txt new file mode 100644 index 0000000000..7dfc202f63 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/attrib_type.txt @@ -0,0 +1,33 @@ +1 SO_accession Sequence Ontology accession +2 SO_term Sequence Ontology term +3 display_term Ensembl display term +4 NCBI_term NCBI term +5 feature_SO_term Sequence Ontology term for the associated feature +6 rank Relative severity of this variation consequence +7 polyphen_prediction PolyPhen-2 prediction +8 sift_prediction SIFT prediction +9 short_name Short name A shorter name for an instance, e.g. a VariationSet +10 dbsnp_clin_sig dbSNP/ClinVar clinical significance The clinical significance of a variant as reported by ClinVar and dbSNP +11 dgva_clin_sig DGVa clinical significance The clinical significance of a structural variant as reported by DGVa +420 clinvar_clin_sig ClinVar clinical significance The clinical significance of a variant as reported by ClinVar +12 prot_func_analysis Protein function analysis The program used to make protein function predictions +13 associated_gene Associated gene ID of gene(s) linked by phenotype association +14 risk_allele Risk allele Risk allele in phenotype association +15 p_value P-value P-value denoting significance of an observed phenotype annotation +16 variation_names Variation names Variant ID(s) linked with a phenotype association +17 sample_id Sample ID Sample ID for source of phenotype association +18 strain_id Strain ID Strain ID for source of phenotype association +19 lod_score LOD score Log Of Odds score +20 variance Variance Variance statistic +21 inheritance_type Inheritance type Inheritance type of a trait +22 external_id External ID External identifier for an entity +23 odds_ratio Odds ratio Odds ratio used to denote significance of an observed phenotype annotation +24 beta_coef Beta coefficient Beta coefficient (or standardized coefficient) used to denote significance of an observed phenotype annotation +25 allele_symbol Allele symbol Allele symbol linked with phenotype association +26 allele_accession_id Allele accession ID Allele accession ID linked with phenotype association +33 marker_accession_id Marker accession ID Marker ID linked with phenotype association +419 evidence Variant evidence status Evidence status for a variant +422 sequence_number Number of sequences in alignment Number of protein sequences in the alignment use to make a protein impact prediction +423 based_on Evidence type used for protein impact prediction Evidence type used for a PolyPhen protein impact prediction +424 conservation_score Sift conservation score Median conservation value in an alignment used to make a Sift prediction +421 review_status ClinVar review_status ClinVar review_status for assertation diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/compressed_genotype_region.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/compressed_genotype_region.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/compressed_genotype_var.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/compressed_genotype_var.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/coord_system.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/coord_system.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/display_group.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/display_group.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/failed_allele.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/failed_allele.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt new file mode 100644 index 0000000000..7e8600477f --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/failed_description.txt @@ -0,0 +1,19 @@ +1 Variant maps to more than 3 different locations +2 None of the variant alleles match the reference allele +3 Variant has more than 3 different alleles +4 Loci with no observed variant alleles in dbSNP +5 Variant does not map to the genome +6 Variant has no genotypes +7 Genotype frequencies do not add up to 1 +8 Variant has no associated sequence +9 Variant submission has been withdrawn by the 1000 genomes project due to high false positive rate +11 Additional submitted allele data from dbSNP does not agree with the dbSNP refSNP alleles +12 Variant has more than 3 different submitted alleles +13 Alleles contain non-nucleotide characters +14 Alleles contain ambiguity codes +15 Mapped position is not compatible with reported alleles +16 Flagged as suspect by dbSNP +17 Variant can not be re-mapped to the current assembly +18 Supporting evidence can not be re-mapped to the current assembly +19 Variant maps to more than one genomic location +20 Variant at first base in sequence diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/failed_structural_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/failed_structural_variation.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/failed_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/failed_variation.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/genotype_code.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/genotype_code.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/individual.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/individual.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/individual_synonym.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/individual_synonym.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/individual_type.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/individual_type.txt new file mode 100644 index 0000000000..6da0c3ddd1 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/individual_type.txt @@ -0,0 +1,4 @@ +1 fully_inbred multiple organisms have the same genome sequence +2 partly_inbred single organisms have reduced genome variability due to human intervention +3 outbred a single organism which breeds freely +4 mutant a single or multiple organisms with the same genome sequence that have a natural or experimentally induced mutation diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt new file mode 100644 index 0000000000..a1df78dac3 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt @@ -0,0 +1,3 @@ +1 \N schema_type variation +2 \N schema_version 84 +3 \N patch patch_83_84_a.sql|schema version diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta_coord.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta_coord.txt new file mode 100644 index 0000000000..1d044f1d37 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta_coord.txt @@ -0,0 +1,3 @@ +variation_feature 1 1000002 +structural_variation_feature 1 1000002 +phenotype_feature 1 1000002 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/motif_feature_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/motif_feature_variation.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt new file mode 100644 index 0000000000..5d21f089e7 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype.txt @@ -0,0 +1,2 @@ +1 \N phenotype \N +2 \N phenotype2 \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature.txt new file mode 100644 index 0000000000..a2a651ab66 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature.txt @@ -0,0 +1,2 @@ +1 1 1 \N Variation rs12345 1 469283 30252800 30252800 1 +2 2 1 \N Variation rs54321 1 469283 30253900 30253900 1 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature_attrib.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/phenotype_feature_attrib.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/population.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/population.txt new file mode 100644 index 0000000000..ed8e12cf23 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/population.txt @@ -0,0 +1 @@ +1 population \N \N 0 \N UNDISPLAYABLE \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/population_genotype.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/population_genotype.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/population_structure.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/population_structure.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/population_synonym.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/population_synonym.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/protein_function_predictions.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/protein_function_predictions.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/protein_function_predictions_attrib.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/protein_function_predictions_attrib.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/publication.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/publication.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/read_coverage.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/read_coverage.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/regulatory_feature_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/regulatory_feature_variation.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/sample.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/sample.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/sample_genotype_multiple_bp.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/sample_genotype_multiple_bp.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/sample_population.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/sample_population.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/seq_region.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/seq_region.txt new file mode 100644 index 0000000000..5411299b20 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/seq_region.txt @@ -0,0 +1 @@ +469283 20 1 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/source.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/source.txt new file mode 100644 index 0000000000..aa9041585a --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/source.txt @@ -0,0 +1 @@ +1 dbSNP \N \N \N \N germline \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/strain_gtype_poly.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/strain_gtype_poly.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation.txt new file mode 100644 index 0000000000..9baa3c0d86 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation.txt @@ -0,0 +1,3 @@ +1 nsv12345 \N 1 \N 208 \N \N 0 0 \N +2 nsv67890 \N 1 \N 208 \N \N 0 1 \N +3 nsv09876 \N 1 \N 114 \N \N 0 0 \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_association.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_association.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt new file mode 100644 index 0000000000..02ddd82bd3 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_feature.txt @@ -0,0 +1,3 @@ +1 469283 \N 30253000 \N \N 30254000 \N 1 1 nsv12345 1 1 208 \N 0 0 \N \N 1 +2 469283 \N 30255000 \N \N 30256000 \N 1 2 nsv67890 1 1 208 \N 0 1 \N \N 1 +3 469283 \N 30257000 \N \N 30258000 \N 1 3 nsv09876 1 1 114 \N 0 0 \N \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_sample.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/structural_variation_sample.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/study.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/study.txt new file mode 100644 index 0000000000..fbb110ae38 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/study.txt @@ -0,0 +1 @@ +1 1 study_name \N \N \N \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/submitter_handle.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/submitter_handle.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/subsnp_handle.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/subsnp_handle.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/tagged_variation_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/tagged_variation_feature.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/tmp_sample_genotype_single_bp.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/tmp_sample_genotype_single_bp.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/transcript_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/transcript_variation.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/translation_md5.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/translation_md5.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation.txt new file mode 100644 index 0000000000..b944dfdf8d --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/variation.txt @@ -0,0 +1,3 @@ +1 1 rs12345 \N \N 0 0 \N \N \N \N \N 1 +2 1 rs67890 \N \N 0 0 \N \N \N \N \N 1 +3 1 rs54321 \N \N 0 1 \N \N \N \N \N 1 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_attrib.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_attrib.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_citation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_citation.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_feature.txt new file mode 100644 index 0000000000..aea759c0f4 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_feature.txt @@ -0,0 +1,3 @@ +1 469283 30252800 30252800 1 1 \N rs12345 1 genotyped 1 intergenic_variant 1 0 0 \N \N \N \N \N \N 1 +2 469283 30252900 30252900 1 2 \N rs67890 1 \N 1 intergenic_variant 1 0 0 \N \N \N \N \N \N 1 +3 469283 30253900 30253900 1 3 \N rs54321 1 \N 1 intergenic_variant 0 1 \N \N \N \N \N \N 1 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_genename.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_genename.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_hgvs.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_hgvs.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set.txt new file mode 100644 index 0000000000..7e4abf84fc --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set.txt @@ -0,0 +1 @@ +1 variation_set \N \N diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structural_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structural_variation.txt new file mode 100644 index 0000000000..e8d2c31aa1 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structural_variation.txt @@ -0,0 +1,2 @@ +1 1 +2 1 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structure.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_structure.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_variation.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_variation.txt new file mode 100644 index 0000000000..e8d2c31aa1 --- /dev/null +++ b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_set_variation.txt @@ -0,0 +1,2 @@ +1 1 +2 1 diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/variation_synonym.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/variation_synonym.txt new file mode 100644 index 0000000000..e69de29bb2 -- GitLab