Commit 6d2d4671 authored by Jessica Severin's avatar Jessica Severin
Browse files

removed pipeline-tables.sql which is compara specific

parent dc33e57c
CREATE TABLE subset (
subset_id int(10) NOT NULL auto_increment,
description varchar(50),
dump_loc varchar(255),
PRIMARY KEY (subset_id)
);
CREATE TABLE subset_member (
subset_id int(10) NOT NULL,
member_id int(10) NOT NULL,
KEY(subset_id),
KEY(member_id)
);
# table identifies the relationship of which gene member, each
# peptide member is derived from
CREATE TABLE member_gene_peptide(
gene_member_id int(10) NOT NULL,
peptide_member_id int(10) NOT NULL,
UNIQUE (gene_member_id, peptide_member_id),
);
------------------------------------------------------------------------------------
--
-- Table structure for table 'genome_db_extn'
--
-- semantics:
-- genome_db_id - foreign key to genome_db table
-- phylum - string to identify homology groupings
-- dblocator - string to identify location of the external genome database (or file).
CREATE TABLE genome_db_extn (
genome_db_id int(10) DEFAULT '0' NOT NULL,
phylum varchar(40) DEFAULT '' NOT NULL,
locator mediumtext,
UNIQUE KEY genome_db_id (genome_db_id)
);
------------------------------------------------------------------------------------
--
-- Table structure for table 'peptide_align_feature'
--
-- overview: This tables stores the raw HSP local alignment results
-- of peptide to peptide alignments returned by a BLAST run
-- it is translated from a FeaturePair object
-- semantics:
-- peptide_align_feature_id - internal id
-- qmember_id - member.member_id of query peptide
-- hmember_id - member.member_id of hit peptide
-- qgenome_db_id - genome_db_id of query peptide (for query optimization)
-- hgenome_db_id - genome_db_id of hit peptide (for query optimization)
-- qstart - start pos in query peptide sequence
-- qend - end pos in query peptide sequence
-- hstart - start pos in hit peptide sequence
-- hend - end pos in hit peptide sequence
-- score - blast score for this HSP
-- evalue - blast evalue for this HSP
-- align_length - alignment length of HSP
-- identical_matches - blast HSP match score
-- positive_matches - blast HSP positive score
-- perc_ident - percent identical matches in the HSP length
-- perc_pos - precent positive matches in the HSP length
-- cigar_line - cigar string coding the actual alignment
CREATE TABLE peptide_align_feature (
peptide_align_feature_id int(10) unsigned NOT NULL auto_increment,
qmember_id int(10) NOT NULL,
hmember_id int(10) NOT NULL,
qgenome_db_id int(10) NOT NULL,
hgenome_db_id int(10) NOT NULL,
analysis_id int(10) NOT NULL,
qstart int(10) DEFAULT '0' NOT NULL,
qend int(10) DEFAULT '0' NOT NULL,
hstart int(11) DEFAULT '0' NOT NULL,
hend int(11) DEFAULT '0' NOT NULL,
score double(16,4) DEFAULT '0.0000' NOT NULL,
evalue varchar(20),
align_length int(10),
identical_matches int(10),
perc_ident int(10),
positive_matches int(10),
perc_pos int(10),
hit_rank int(10),
cigar_line mediumtext,
PRIMARY KEY (peptide_align_feature_id),
KEY qmember_id (qmember_id),
KEY hmember_id (hmember_id)
);
------------------------------------------------------------------------------------
--
-- Table structure for table 'analysis'
--
-- semantics:
-- analysis_id - internal id
-- created - date to distinguish newer and older versions off the
-- same analysis. Not well maintained so far.
-- logic_name string to identify the analysis. Used mainly inside pipeline.
-- db, db_version, db_file
-- - db should be a database name, db version the version of that db
-- db_file the file system location of that database,
-- probably wiser to generate from just db and configurations
-- program, program_version,program_file
-- - The binary used to create a feature. Similar semantic to above
-- module, module_version
-- - Perl module names (RunnableDBS usually) executing this analysis.
-- parameters a paramter string which is processed by the perl module
-- gff_source, gff_feature
-- - how to make a gff dump from features with this analysis
CREATE TABLE analysis (
analysis_id int(10) unsigned DEFAULT '0' NOT NULL auto_increment,
created datetime DEFAULT '0000-00-00 00:00:00' NOT NULL,
logic_name varchar(40) not null,
db varchar(120),
db_version varchar(40),
db_file varchar(120),
program varchar(80),
program_version varchar(40),
program_file varchar(80),
parameters varchar(255),
module varchar(80),
module_version varchar(40),
gff_source varchar(40),
gff_feature varchar(40),
status enum('BLOCKED', 'READY','WORKING','DONE') DEFAULT 'READY' NOT NULL,
PRIMARY KEY (analysis_id),
KEY logic_name_idx( logic_name ),
UNIQUE(logic_name)
);
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