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Commit 6c5b0e50 authored by Alessandro Vullo's avatar Alessandro Vullo
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[ENSCORESW-2299]. Patching test DBs with update to hit_name.

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modules/t/test-genome-DBs/circ/core/meta.txt
View file @ 6c5b0e50
......@@ -109,3 +109,4 @@
109 \N patch patch_88_89_a.sql|schema_version
110 \N patch patch_89_90_a.sql|schema_version
111 \N patch patch_89_90_b.sql|remove_status
112 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/circ/core/table.sql
View file @ 6c5b0e50
......@@ -476,7 +476,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=112 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=113 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -655,7 +655,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
View file @ 6c5b0e50
......@@ -88,3 +88,4 @@
155 \N patch patch_88_89_a.sql|schema_version
156 \N patch patch_89_90_a.sql|schema_version
157 \N patch patch_89_90_b.sql|remove_status
158 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
View file @ 6c5b0e50
......@@ -476,7 +476,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=158 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=159 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -655,7 +655,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
View file @ 6c5b0e50
......@@ -88,3 +88,4 @@
137 \N patch patch_88_89_a.sql|schema_version
138 \N patch patch_89_90_a.sql|schema_version
139 \N patch patch_89_90_b.sql|remove_status
140 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
View file @ 6c5b0e50
......@@ -476,7 +476,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=140 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=141 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -655,7 +655,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
View file @ 6c5b0e50
......@@ -93,3 +93,4 @@
2100 \N patch patch_88_89_a.sql|schema_version
2101 \N patch patch_89_90_a.sql|schema_version
2102 \N patch patch_89_90_b.sql|remove_status
2103 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
View file @ 6c5b0e50
......@@ -476,7 +476,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=2103 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=2104 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -655,7 +655,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
View file @ 6c5b0e50
1 \N schema_type variation
2 \N schema_version 89
2 \N schema_version 90
3 \N patch patch_84_85_a.sql|schema version
4 \N patch patch_84_85_b.sql|create sample_synonym
5 \N patch patch_84_85_c.sql|drop column moltype from variation_synonym
......@@ -18,3 +18,6 @@
18 \N patch patch_87_88_b.sql|seq_region_name_255
19 \N patch patch_88_89_a.sql|schema version
20 \N patch patch_88_89_b.sql|Drop strain_gtype_poly table
21 \N patch patch_89_90_a.sql|schema version
22 \N patch patch_89_90_b.sql|add start_retained_variant to consequence_types in variation_feature and transcript_variation
23 \N patch patch_89_90_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
View file @ 6c5b0e50
......@@ -168,7 +168,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=21 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=24 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -513,7 +513,7 @@ CREATE TABLE `transcript_variation` (
`feature_stable_id` varchar(128) DEFAULT NULL,
`allele_string` text,
`somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','protein_altering_variant') DEFAULT NULL,
`consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
`cds_start` int(11) unsigned DEFAULT NULL,
`cds_end` int(11) unsigned DEFAULT NULL,
`cdna_start` int(11) unsigned DEFAULT NULL,
......@@ -589,7 +589,7 @@ CREATE TABLE `variation_feature` (
`map_weight` int(11) NOT NULL,
`flags` set('genotyped') DEFAULT NULL,
`source_id` int(10) unsigned NOT NULL,
`consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant') NOT NULL DEFAULT 'intergenic_variant',
`consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
`class_attrib_id` int(10) unsigned DEFAULT '0',
`somatic` tinyint(1) NOT NULL DEFAULT '0',
......
modules/t/test-genome-DBs/mapping/core/meta.txt
View file @ 6c5b0e50
......@@ -49,3 +49,4 @@
142 \N patch patch_88_89_a.sql|schema_version
143 \N patch patch_89_90_a.sql|schema_version
144 \N patch patch_89_90_b.sql|remove_status
145 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/mapping/core/table.sql
View file @ 6c5b0e50
......@@ -476,7 +476,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=145 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=146 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -655,7 +655,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
modules/t/test-genome-DBs/multi/compara/meta.txt
View file @ 6c5b0e50
33 \N schema_version 89
36 \N schema_version 90
2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr
......@@ -29,3 +29,9 @@
32 \N patch patch_87_88_i.sql|genome_db.display_name
34 \N patch patch_88_89_a.sql|schema_version
35 \N patch patch_88_89_b.sql|genomic_align_tree_parent_id_null
37 \N patch patch_89_90_a.sql|schema_version
38 \N patch patch_89_90_b.sql|genomic_align_tree_parent_id_null
39 \N patch patch_89_90_c.sql|constrained_element_pvalue_not_null
40 \N patch patch_89_90_d.sql|genomic_align_tree_left_node_id_null
41 \N patch patch_89_90_e.sql|seq_member_projection
42 \N patch patch_89_90_f.sql|gene_member_missing_biotype_groups
modules/t/test-genome-DBs/multi/compara/table.sql
View file @ 6c5b0e50
......@@ -36,7 +36,7 @@ CREATE TABLE `constrained_element` (
`dnafrag_end` int(12) unsigned NOT NULL,
`dnafrag_strand` int(2) NOT NULL,
`method_link_species_set_id` int(10) unsigned NOT NULL,
`p_value` double DEFAULT NULL,
`p_value` double NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
KEY `dnafrag_id` (`dnafrag_id`),
KEY `constrained_element_id_idx` (`constrained_element_id`),
......@@ -139,7 +139,7 @@ CREATE TABLE `gene_member` (
`source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
`biotype_group` enum('coding','snoncoding','lnoncoding','mnoncoding','LRG') NOT NULL DEFAULT 'coding',
`biotype_group` enum('coding','pseudogene','snoncoding','lnoncoding','mnoncoding','LRG','undefined','no_group','current_notdumped','notcurrent') NOT NULL DEFAULT 'coding',
`canonical_member_id` int(10) unsigned DEFAULT NULL,
`description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
......@@ -334,8 +334,8 @@ CREATE TABLE `genomic_align_tree` (
`root_id` bigint(20) unsigned NOT NULL DEFAULT '0',
`left_index` int(10) NOT NULL DEFAULT '0',
`right_index` int(10) NOT NULL DEFAULT '0',
`left_node_id` bigint(10) NOT NULL DEFAULT '0',
`right_node_id` bigint(10) NOT NULL DEFAULT '0',
`left_node_id` bigint(10) DEFAULT NULL,
`right_node_id` bigint(10) DEFAULT NULL,
`distance_to_parent` double NOT NULL DEFAULT '1',
PRIMARY KEY (`node_id`),
KEY `parent_id` (`parent_id`),
......@@ -434,7 +434,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255))
) ENGINE=MyISAM AUTO_INCREMENT=36 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=43 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -565,6 +565,21 @@ CREATE TABLE `seq_member` (
KEY `seq_member_gene_member_id_end` (`seq_member_id`,`gene_member_id`)
) ENGINE=MyISAM AUTO_INCREMENT=100289438 DEFAULT CHARSET=latin1 MAX_ROWS=100000000;
CREATE TABLE `seq_member_projection` (
`target_seq_member_id` int(10) unsigned NOT NULL,
`source_seq_member_id` int(10) unsigned NOT NULL,
`identity` float(5,2) NOT NULL,
PRIMARY KEY (`target_seq_member_id`),
KEY `source_seq_member_id` (`source_seq_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `seq_member_projection_stable_id` (
`target_seq_member_id` int(10) unsigned NOT NULL,
`source_stable_id` varchar(128) NOT NULL,
PRIMARY KEY (`target_seq_member_id`),
KEY `source_stable_id` (`source_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `sequence` (
`sequence_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`length` int(10) NOT NULL,
......
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
View file @ 6c5b0e50
......@@ -166,3 +166,4 @@
1678 \N patch patch_88_89_a.sql|schema_version
1679 \N patch patch_89_90_a.sql|schema_version
1680 \N patch patch_89_90_b.sql|remove_status
1681 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/mus_musculus/core/table.sql
View file @ 6c5b0e50
......@@ -476,7 +476,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=1681 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=1682 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -655,7 +655,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
View file @ 6c5b0e50
1 \N schema_type variation
2 \N schema_version 89
2 \N schema_version 90
6 1 species.production_name mus_musculus
15 1 web_config sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
14 1 web_config set#All failed variants#All failed variants#variation_set_fail_all#failed
......@@ -45,3 +45,6 @@
51 \N patch patch_87_88_b.sql|seq_region_name_255
52 \N patch patch_88_89_a.sql|schema version
53 \N patch patch_88_89_b.sql|Drop strain_gtype_poly table
54 \N patch patch_89_90_a.sql|schema version
55 \N patch patch_89_90_b.sql|add start_retained_variant to consequence_types in variation_feature and transcript_variation
56 \N patch patch_89_90_c.sql|remove regulatory and TFBS consequences from consequence_types in transcript_variation
modules/t/test-genome-DBs/mus_musculus/variation/table.sql
View file @ 6c5b0e50
......@@ -168,7 +168,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=52 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=57 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) NOT NULL,
......@@ -519,7 +519,7 @@ CREATE TABLE `transcript_variation` (
`feature_stable_id` varchar(128) DEFAULT NULL,
`allele_string` text,
`somatic` tinyint(1) NOT NULL DEFAULT '0',
`consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','protein_altering_variant') DEFAULT NULL,
`consequence_types` set('splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','feature_elongation','feature_truncation','protein_altering_variant','start_retained_variant') DEFAULT NULL,
`cds_start` int(11) unsigned DEFAULT NULL,
`cds_end` int(11) unsigned DEFAULT NULL,
`cdna_start` int(11) unsigned DEFAULT NULL,
......@@ -595,7 +595,7 @@ CREATE TABLE `variation_feature` (
`map_weight` int(11) NOT NULL,
`flags` set('genotyped') DEFAULT NULL,
`source_id` int(10) unsigned NOT NULL,
`consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant') NOT NULL DEFAULT 'intergenic_variant',
`consequence_types` set('intergenic_variant','splice_acceptor_variant','splice_donor_variant','stop_lost','coding_sequence_variant','missense_variant','stop_gained','synonymous_variant','frameshift_variant','non_coding_transcript_variant','non_coding_transcript_exon_variant','mature_miRNA_variant','NMD_transcript_variant','5_prime_UTR_variant','3_prime_UTR_variant','incomplete_terminal_codon_variant','intron_variant','splice_region_variant','downstream_gene_variant','upstream_gene_variant','start_lost','stop_retained_variant','inframe_insertion','inframe_deletion','transcript_ablation','transcript_fusion','transcript_amplification','transcript_translocation','TFBS_ablation','TFBS_fusion','TFBS_amplification','TFBS_translocation','regulatory_region_ablation','regulatory_region_fusion','regulatory_region_amplification','regulatory_region_translocation','feature_elongation','feature_truncation','regulatory_region_variant','TF_binding_site_variant','protein_altering_variant','start_retained_variant') NOT NULL DEFAULT 'intergenic_variant',
`variation_set_id` set('1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','25','26','27','28','29','30','31','32','33','34','35','36','37','38','39','40','41','42','43','44','45','46','47','48','49','50','51','52','53','54','55','56','57','58','59','60','61','62','63','64') NOT NULL DEFAULT '',
`class_attrib_id` int(10) unsigned DEFAULT '0',
`somatic` tinyint(1) NOT NULL DEFAULT '0',
......
modules/t/test-genome-DBs/nameless/core/meta.txt
View file @ 6c5b0e50
......@@ -87,3 +87,4 @@
141 \N patch patch_88_89_a.sql|schema_version
142 \N patch patch_89_90_a.sql|schema_version
143 \N patch patch_89_90_b.sql|remove_status
144 \N patch patch_89_90_c.sql|pf_hit_name_case_sensitive
modules/t/test-genome-DBs/nameless/core/table.sql
View file @ 6c5b0e50
......@@ -466,7 +466,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
KEY `species_value_idx` (`species_id`,`meta_value`)
) ENGINE=MyISAM AUTO_INCREMENT=144 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=145 DEFAULT CHARSET=latin1;
CREATE TABLE `meta_coord` (
`table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
......@@ -645,7 +645,7 @@ CREATE TABLE `protein_feature` (
`seq_end` int(10) NOT NULL DEFAULT '0',
`hit_start` int(10) NOT NULL DEFAULT '0',
`hit_end` int(10) NOT NULL DEFAULT '0',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
`hit_name` varchar(40) COLLATE latin1_bin NOT NULL,
`analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
`score` double NOT NULL DEFAULT '0',
`evalue` double DEFAULT NULL,
......
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