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[Raisinbread] Added CNV/CPG records for candidates with SNP data
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@AlexandraLivadas
AlexandraLivadas committed Aug 12, 2020
1 parent 53979f0 commit 7c4eb4d
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25 changes: 25 additions & 0 deletions SQL/New_patches/2020-08-12_add_CNV_CPG_data_for_genomic_browser.sql
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--Add CNV data for some candidates
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, '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 (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);

--Add CPG data for some candidates
--Add data to genomic_sample_candidate_rel to match CPG to Candidate
INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573847', 300165);
INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573848', 300165);
INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573851', 300162);
INSERT INTO `genomic_sample_candidate_rel` (`sample_label`, `CandID`) VALUES ('sl573852', 300139);

--Add data to genomic_cpg_annotation
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);

--Add data to gemonic_cpg
--The beta_value was added because it cannot be null
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);
4 changes: 4 additions & 0 deletions raisinbread/RB_files/RB_CNV.sql
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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;
4 changes: 4 additions & 0 deletions raisinbread/RB_files/RB_genomic_cpg.sql
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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;
4 changes: 4 additions & 0 deletions raisinbread/RB_files/RB_genomic_cpg_annotation.sql
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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;
4 changes: 4 additions & 0 deletions raisinbread/RB_files/RB_genomic_sample_candidate_rel.sql
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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;

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