From ca29c6f931310684caf5dc8cc6447f6ac7293856 Mon Sep 17 00:00:00 2001 From: Alexandra Livadas Date: Wed, 19 Aug 2020 15:14:42 -0400 Subject: [PATCH] [Raisinbread] Added CNV/CPG records for candidates with SNP data (#6900) Added CNV and CPG records for candidates that already have SNP data. This is necessary so that the CNV and Methylation tabs in the Genomic Browser module can be tested. Resolves #6881 Partially resolves #6302 --- raisinbread/RB_files/RB_CNV.sql | 4 ++++ raisinbread/RB_files/RB_genomic_cpg.sql | 4 ++++ raisinbread/RB_files/RB_genomic_cpg_annotation.sql | 4 ++++ raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql | 4 ++++ 4 files changed, 16 insertions(+) diff --git a/raisinbread/RB_files/RB_CNV.sql b/raisinbread/RB_files/RB_CNV.sql index 9a5da414fb1..40ff309e057 100644 --- a/raisinbread/RB_files/RB_CNV.sql +++ b/raisinbread/RB_files/RB_CNV.sql @@ -1,5 +1,9 @@ SET FOREIGN_KEY_CHECKS=0; TRUNCATE TABLE `CNV`; LOCK TABLES `CNV` WRITE; +INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (1,300165,NULL,'gain',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','+',11007,11008,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (2,300165,NULL,'unknown',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','-',11009,11010,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (3,300141,NULL,'unknown',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','+',11007,11008,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `CNV` (`CNVID`, `CandID`, `Description`, `Type`, `EventName`, `Common_CNV`, `Characteristics`, `CopyNumChange`, `Inheritance`, `ArrayReport`, `Markers`, `ArrayReportDetail`, `ValidationMethod`, `PlatformID`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`, `Symbol`, `Name`, `NCBIID`, `OfficialSymbol`, `OfficialName`) VALUES (4,300162,NULL,'unknown',NULL,'Y','Unknown',NULL,'unknown','Normal',NULL,NULL,NULL,1,'chr1','+',11007,11008,NULL,NULL,NULL,NULL,NULL); UNLOCK TABLES; SET FOREIGN_KEY_CHECKS=1; diff --git a/raisinbread/RB_files/RB_genomic_cpg.sql b/raisinbread/RB_files/RB_genomic_cpg.sql index f9f7fdd9753..63af9bf214e 100644 --- a/raisinbread/RB_files/RB_genomic_cpg.sql +++ b/raisinbread/RB_files/RB_genomic_cpg.sql @@ -1,5 +1,9 @@ SET FOREIGN_KEY_CHECKS=0; TRUNCATE TABLE `genomic_cpg`; LOCK TABLES `genomic_cpg` WRITE; +INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573847','CPG_573847',1.000); +INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573848','CPG_573848',1.000); +INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573851','CPG_573851',1.000); +INSERT INTO `genomic_cpg` (`sample_label`, `cpg_name`, `beta_value`) VALUES ('sl573852','CPG_573852',1.000); UNLOCK TABLES; SET FOREIGN_KEY_CHECKS=1; diff --git a/raisinbread/RB_files/RB_genomic_cpg_annotation.sql b/raisinbread/RB_files/RB_genomic_cpg_annotation.sql index 67fe17c80bb..124d3d1cd8c 100644 --- a/raisinbread/RB_files/RB_genomic_cpg_annotation.sql +++ b/raisinbread/RB_files/RB_genomic_cpg_annotation.sql @@ -1,5 +1,9 @@ SET FOREIGN_KEY_CHECKS=0; TRUNCATE TABLE `genomic_cpg_annotation`; LOCK TABLES `genomic_cpg_annotation` WRITE; +INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573847',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008); +INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573848',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008); +INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573851',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008); +INSERT INTO `genomic_cpg_annotation` (`cpg_name`, `address_id_a`, `probe_seq_a`, `address_id_b`, `probe_seq_b`, `design_type`, `color_channel`, `genome_build`, `probe_snp_10`, `gene_name`, `gene_acc_num`, `gene_group`, `island_loc`, `island_relation`, `fantom_promoter_loc`, `dmr`, `enhancer`, `hmm_island_loc`, `reg_feature_loc`, `reg_feature_group`, `dhs`, `platform_id`, `Chromosome`, `Strand`, `EndLoc`, `StartLoc`) VALUES ('CPG_573852',NULL,NULL,NULL,NULL,NULL,'Red',NULL,NULL,NULL,NULL,NULL,NULL,'island',NULL,'DMR',NULL,NULL,NULL,NULL,NULL,1,'chr1','+',11007,11008); UNLOCK TABLES; SET FOREIGN_KEY_CHECKS=1; diff --git a/raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql b/raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql index 858ea25d6f5..b35a5a11070 100644 --- a/raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql +++ b/raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql @@ -1,5 +1,9 @@ SET FOREIGN_KEY_CHECKS=0; TRUNCATE TABLE `genomic_sample_candidate_rel`; LOCK TABLES `genomic_sample_candidate_rel` WRITE; +INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573852',300139); +INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573851',300162); +INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573847',300165); +INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573848',300165); UNLOCK TABLES; SET FOREIGN_KEY_CHECKS=1;