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ensembl-gh-mirror
ensembl
Commits
6c5b0e50
Commit
6c5b0e50
authored
Jul 04, 2017
by
Alessandro Vullo
Browse files
[
ENSCORESW-2299
]. Patching test DBs with update to hit_name.
parent
b3694c99
Changes
24
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20 changed files
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62 additions
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28 deletions
+62
-28
modules/t/test-genome-DBs/circ/core/meta.txt
modules/t/test-genome-DBs/circ/core/meta.txt
+1
-0
modules/t/test-genome-DBs/circ/core/table.sql
modules/t/test-genome-DBs/circ/core/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+1
-0
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+2
-2
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+4
-1
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+3
-3
modules/t/test-genome-DBs/mapping/core/meta.txt
modules/t/test-genome-DBs/mapping/core/meta.txt
+1
-0
modules/t/test-genome-DBs/mapping/core/table.sql
modules/t/test-genome-DBs/mapping/core/table.sql
+2
-2
modules/t/test-genome-DBs/multi/compara/meta.txt
modules/t/test-genome-DBs/multi/compara/meta.txt
+7
-1
modules/t/test-genome-DBs/multi/compara/table.sql
modules/t/test-genome-DBs/multi/compara/table.sql
+20
-5
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+1
-0
modules/t/test-genome-DBs/mus_musculus/core/table.sql
modules/t/test-genome-DBs/mus_musculus/core/table.sql
+2
-2
modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
+4
-1
modules/t/test-genome-DBs/mus_musculus/variation/table.sql
modules/t/test-genome-DBs/mus_musculus/variation/table.sql
+3
-3
modules/t/test-genome-DBs/nameless/core/meta.txt
modules/t/test-genome-DBs/nameless/core/meta.txt
+1
-0
modules/t/test-genome-DBs/nameless/core/table.sql
modules/t/test-genome-DBs/nameless/core/table.sql
+2
-2
No files found.
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
=
11
2
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
11
3
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
=
15
8
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
15
9
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
=
14
0
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
14
1
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
=
210
3
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
210
4
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
8
9
2 \N schema_version 9
0
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
=
2
1
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
2
4
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
=
14
5
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
14
6
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
3
3
\N schema_version
8
9
3
6
\N schema_version 9
0
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
=
3
6
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
4
3
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
=
168
1
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
168
2
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
8
9
2 \N schema_version 9
0
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
=
5
2
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
5
7
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
=
14
4
DEFAULT
CHARSET
=
latin1
;
)
ENGINE
=
MyISAM
AUTO_INCREMENT
=
14
5
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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