Keeping sql and txt unzipped now for better maintainabillity in cvs

modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.sql

+CREATE TABLE `alt_allele` (
+  `alt_allele_id` int(11) NOT NULL auto_increment,
+  `gene_id` int(11) NOT NULL default '0',
+  UNIQUE KEY `gene_idx` (`gene_id`),
+  UNIQUE KEY `allele_idx` (`alt_allele_id`,`gene_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.txt

+1	18256
+1	18257
+1	18258
+1	18259

modules/t/test-genome-DBs/homo_sapiens/core/analysis.sql

+CREATE TABLE `analysis` (
+  `analysis_id` int(10) unsigned NOT NULL auto_increment,
+  `created` datetime NOT NULL default '0000-00-00 00:00:00',
+  `logic_name` varchar(40) collate latin1_bin NOT NULL default '',
+  `db` varchar(120) collate latin1_bin default NULL,
+  `db_version` varchar(40) collate latin1_bin default NULL,
+  `db_file` varchar(120) collate latin1_bin default NULL,
+  `program` varchar(80) collate latin1_bin default NULL,
+  `program_version` varchar(40) collate latin1_bin default NULL,
+  `program_file` varchar(80) collate latin1_bin default NULL,
+  `parameters` varchar(255) collate latin1_bin default NULL,
+  `module` varchar(80) collate latin1_bin default NULL,
+  `module_version` varchar(40) collate latin1_bin default NULL,
+  `gff_source` varchar(40) collate latin1_bin default NULL,
+  `gff_feature` varchar(40) collate latin1_bin default NULL,
+  PRIMARY KEY  (`analysis_id`),
+  UNIQUE KEY `logic_name` (`logic_name`),
+  KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt

+1	2000-09-08 16:10:03	RepeatMask	repbase	001212		RepeatMasker	1			RepeatMasker	1	RepeatMasker	repeat
+2	2000-09-22 10:59:05	Genscan	HumanIso.smat	1	HumanIso.smat	genscan	1.0			Genscan	1	genscan	prediction
+5	2000-09-28 17:33:27	Swall	swall	1	swall	wublastp	1		-hitdist=40, -cpus=1	BlastGenscanPep		wublastp	similarity
+7	2000-10-09 15:30:14	Vertrna	embl_vertrna	1	embl_vertrna	wutblastn	1		-hitdist=40, -cpus=1	BlastGenscanDNA	1	wutblastn	similarity
+4	2000-12-18 15:12:30	tRNAscan	tRNA	1		tRNAscan-SE	1.11			tRNAscan_SE	1	tRNAscan-SE	tRNA
+8	2000-12-18 18:28:03	CpG	cpg	1		cpg	1			CPG	1	cpg	cpg_island
+9	2001-01-15 17:00:00	Unigene	unigene.seq	1	unigene.seq	wutblastn	1		-hitdist=40, -cpus=1	BlastGenscanDNA	1	wutblastn	similarity
+10	2001-01-15 17:00:00	QTL		1			1			QtlPlacer	1	experimental	marker
+12	2001-03-28 16:42:32	dbEST	dbEST	1	dbEST	wutblastn	1		-hitdist=40, -cpus=1	BlastGenscanDNA	1	wutblastn	similarity
+6	2001-09-04 17:21:19	Eponine	NULL	NULL	NULL	eponine-scan	1	/usr/opt/java131/bin/java	-epojar => /usr/local/ensembl/lib/eponine-scan.jar, -threshold => 0.999	VC_EponineTSS	1	Eponine	TSS
+54	2002-08-12 14:52:26	human_swall_protein		1		TGE_gw	1			TargettedGeneWise		TGE_gw	gene
+53	2002-08-12 14:52:26	human_refseq_protein		1		TGE_gw	1			TargettedGeneWise		TGE_gw	gene
+1280	2002-08-12 14:52:26	other_swall_protein		1		similarity_genewise	1			FPC_BlastMiniGenewise		similarity_genewise	gene
+1281	2002-08-12 14:52:26	combined-protein_cdna		1		combined_gw_e2g	1			Combine_Genewises_and_E2Gs		combined_gw_e2g	gene
+1282	2002-08-12 14:52:26	ensembl		1		ensembl	1			Gene_Builder		ensembl	gene
+1290	2002-08-12 14:52:26	refseq_cdna	human_mRNA	1		exonerate_e2g	1			FilterESTs_and_E2G		exonerate	gene
+1291	2002-08-12 14:52:26	embl_vertrna	human_mRNA	1		exonerate_e2g	1			FilterESTs_and_E2G		exonerate	gene
+49	0000-00-00 00:00:00	Pfam	Pfam	1	/data/blastdb/Ensembl/Pfam_ls;/data/blastdb/Ensembl/Pfam_fs	/nfs/farm/Worms/bin/hmmpfam	1	/nfs/farm/Worms/bin/hmmpfam		Pfam	1	PFAM	domain
+40	0000-00-00 00:00:00	prints	prints	NULL	/acari/analysis/iprscan/data/prints.pval	/acari/analysis/iprscan/bin/OSF1/FingerPRINTScan	NULL	/acari/analysis/iprscan/bin/OSF1/FingerPRINTScan	NULL	Prints	NULL	PRINTS	domain
+41	0000-00-00 00:00:00	pfscan	pfscan	NULL	/acari/analysis/iprscan/data/prosite_prerelease.prf	/acari/analysis/iprscan/bin/OSF1/pfscan	NULL	/acari/analysis/iprscan/bin/OSF1/pfscan	NULL	Profile	NULL	PROFILE	domain
+43	0000-00-00 00:00:00	Signalp	signal_peptide	NULL	NULL	/usr/local/ensembl/bin/signalp	NULL	/usr/local/ensembl/bin/signalp	NULL	Signalp	NULL	Signalp	annot
+46	0000-00-00 00:00:00	tmhmm	transmembrane	NULL	NULL	/acari/work1/mongin/src/pipeline4anopheles/scripts/protein_pipeline/run_tmhmm	NULL	/acari/work1/mongin/src/pipeline4anopheles/scripts/protein_pipeline/run_tmhmm	NULL	Tmhmm	NULL	Tmhmm	annot
+45	0000-00-00 00:00:00	ncoils	coiled_coil	NULL	NULL	/usr/local/ensembl/bin/ncoils	NULL	/usr/local/ensembl/bin/ncoils	NULL	ncoils	NULL	ncoils	annot
+44	0000-00-00 00:00:00	Seg	low_complexity	NULL	NULL	/usr/local/ensembl/bin/seg	NULL	/usr/local/ensembl/bin/seg	NULL	Seg	NULL	Seg	annot
+42	0000-00-00 00:00:00	scanprosite	prosite	NULL	/acari/analysis/iprscan/data/prosite.patterns	/acari/analysis/iprscan/bin/scanregexpf.pl	/acari/analysis/iprscan/data/confirm.pat	/acari/analysis/iprscan/bin/scanregexpf.pl		Prosite	NULL	PROSITE	domain
+71	0000-00-00 00:00:00	Superfamily	Superfamily	1	/data/blastdb/Ensembl/sam/superfamily	/acari/work1/mongin/superfamily/superfamily.pl	1	/acari/work1/mongin/superfamily/superfamily.pl		Superfamily	1	Superfamily	annot
+1292	0000-00-00 00:00:00	SNPDensity	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N
+1293	0000-00-00 00:00:00	RepeatCoverage	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N
+1500	0000-00-00 00:00:00	miRanda	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N
+1501	0000-00-00 00:00:00	cisred	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N
+1502	0000-00-00 00:00:00	cisred_search	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N
+1503	0000-00-00 00:00:00	DitagAlign	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N

modules/t/test-genome-DBs/homo_sapiens/core/analysis_description.sql

+CREATE TABLE `analysis_description` (
+  `analysis_id` int(10) unsigned NOT NULL default '0',
+  `description` text collate latin1_bin,
+  `display_label` varchar(255) collate latin1_bin default NULL,
+  `displayable` BOOLEAN NOT NULL DEFAULT 1,
+  `web_data` TEXT,
+
+  KEY `analysis_idx` (`analysis_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/analysis_description.txt

+1282	Genes were annotated by the Ensembl automatic analysis pipeline using either a GeneWise model from a human/vertebrate protein, a set of aligned human cDNAs followed by GenomeWise for ORF prediction or from Genscan exons supported by protein, cDNA and EST evidence. GeneWise models are further combined with available aligned cDNAs to annotate UTRs.	ensembl transcript 1 web data 1
+1503	new description	new label   0	    web data 2
+1504	updated description	\N  0	    web data 3

modules/t/test-genome-DBs/homo_sapiens/core/assembly.sql

+CREATE TABLE `assembly` (
+  `asm_seq_region_id` int(10) unsigned NOT NULL default '0',
+  `cmp_seq_region_id` int(10) unsigned NOT NULL default '0',
+  `asm_start` int(10) NOT NULL default '0',
+  `asm_end` int(10) NOT NULL default '0',
+  `cmp_start` int(10) NOT NULL default '0',
+  `cmp_end` int(10) NOT NULL default '0',
+  `ori` tinyint(4) NOT NULL default '0',
+  KEY `cmp_seq_region_id` (`cmp_seq_region_id`),
+  KEY `asm_seq_region_id` (`asm_seq_region_id`,`asm_start`),
+  UNIQUE KEY all_idx (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/assembly.txt

+469283	317101	30263615	30426490	101	162976	1
+469283	317332	30811187	30929959	101	118873	1
+469283	317348	31086734	31205532	101	118899	1
+469283	317523	30451401	30562994	101	111694	1
+469283	318770	30726577	30811186	101	84710	1
+469283	319047	30562995	30708200	101	145306	1
+469283	319456	30993469	31086733	101	93365	1
+469283	339816	30426491	30451400	101	25010	1
+469283	345105	30708201	30726576	1	18376	1
+469283	368744	30249935	30263614	101	13780	1
+469283	376992	31205533	31254640	101	49208	1
+469283	469270	30929960	30993468	101	63609	1
+469341	376992	1	49208	1	49208	1
+469339	318770	1	84710	1	84710	1
+469336	345105	1	18376	1	18376	1
+469335	319456	1	93365	1	93365	1
+469343	469270	1	63609	1	63609	1
+469333	317523	1	111694	1	111694	1
+469340	339816	1	25010	1	25010	1
+469342	319047	1	145414	1	145414	1
+469338	368744	1	13780	1	13780	1
+469332	317348	1	118899	1	118899	1
+469334	317101	1	162976	1	162976	1
+469337	317332	1	118873	1	118873	1
+469348	368744	657970	671649	101	13780	1
+469348	317101	671650	834525	101	162976	1
+469348	339816	834526	859435	101	25010	1
+469348	317523	859436	971029	101	111694	1
+469348	319047	971030	1116235	101	145306	1
+469348	345105	1116236	1134611	1	18376	1
+469348	318770	1134612	1219221	101	84710	1
+469348	317332	1219222	1337994	101	118873	1
+469348	469270	1337995	1401503	101	63609	1
+469348	319456	1401504	1494768	101	93365	1
+469348	317348	1494769	1613567	101	118899	1
+469348	376992	1613568	1662675	101	49208	1
+965899	965888	1	16571	1	16571	1
+469271	965905	1	200	10	209	1
+469271	965905	201	400	401	600	-1
+469282	965905	1	100	701	800	-1
+965906	469283	563	3444	31222465	31225346	1
+965906	469283	397	562	31214121	31214286	1
+965906	469283	100	396	31210077	31210373	1

modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.sql

+CREATE TABLE `assembly_exception` (
+  `assembly_exception_id` int(10) unsigned NOT NULL auto_increment,
+  `seq_region_id` int(11) NOT NULL default '0',
+  `seq_region_start` int(11) NOT NULL default '0',
+  `seq_region_end` int(11) NOT NULL default '0',
+  `exc_type` enum('HAP','PAR') collate latin1_bin NOT NULL default 'HAP',
+  `exc_seq_region_id` int(11) NOT NULL default '0',
+  `exc_seq_region_start` int(11) NOT NULL default '0',
+  `exc_seq_region_end` int(11) NOT NULL default '0',
+  `ori` int(11) NOT NULL default '0',
+  PRIMARY KEY  (`assembly_exception_id`),
+  KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
+  KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.txt

+1	469294	10000000	10500000	PAR	469283	30300000	30800000	1
+2	469351	30500000	30599999	HAP	469283	30500000	30699999	1

modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.sql

+CREATE TABLE `attrib_type` (
+  `attrib_type_id` smallint(5) unsigned NOT NULL auto_increment,
+  `code` varchar(15) collate latin1_bin NOT NULL default '',
+  `name` varchar(255) collate latin1_bin NOT NULL default '',
+  `description` text collate latin1_bin,
+  PRIMARY KEY  (`attrib_type_id`),
+  UNIQUE KEY `c` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt

+1	synonym	Alternate names for clone	Synonyms
+2	FISHmap	FISH information	FISH map
+3	organisation	Organisation sequencing clone	
+4	state	Current state of clone	
+5	BACend_flag	BAC end flags	
+6	embl_acc	EMBL accession number	
+7	superctg	Super contig id.	
+8	seq_len	Accession length	
+9	fp_size	FP size	
+10	note	Note	
+11	positioned_by	Positioned by	
+12	bac_acc	BAC end accession	
+13	htg_phase	HTG Phase	High Throughput Genome Phase
+14	toplevel	Top Level	Top Level Non-Redundant Sequence Region
+15	_rna_edit	RNA editing	\N
+16	_selenocysteine	Selenocysteine	\N
+17	codon_table	Codon Table	Alternate codon table

modules/t/test-genome-DBs/homo_sapiens/core/coord_system.sql

+CREATE TABLE `coord_system` (
+  `coord_system_id` int(11) NOT NULL auto_increment,
+  `name` varchar(40) collate latin1_bin NOT NULL default '',
+  `version` varchar(40) collate latin1_bin default NULL,
+  `rank` int(11) NOT NULL default '0',
+  `attrib` set('default_version','sequence_level') collate latin1_bin default NULL,
+  PRIMARY KEY  (`coord_system_id`),
+  UNIQUE KEY `rank` (`rank`),
+  UNIQUE KEY `name` (`name`,`version`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/coord_system.txt

+1	chromosome	NCBI33	1	default_version
+2	supercontig	\N	2	default_version
+3	clone	\N	3	default_version
+4	contig	\N	4	default_version,sequence_level
+6	chunk	\N	5	default_version
+7	alt_chrom	\N	6	default_version

modules/t/test-genome-DBs/homo_sapiens/core/density_feature.sql

+CREATE TABLE `density_feature` (
+  `density_feature_id` int(11) NOT NULL auto_increment,
+  `density_type_id` int(11) NOT NULL default '0',
+  `seq_region_id` int(11) NOT NULL default '0',
+  `seq_region_start` int(11) NOT NULL default '0',
+  `seq_region_end` int(11) NOT NULL default '0',
+  `density_value` float NOT NULL default '0',
+  PRIMARY KEY  (`density_feature_id`),
+  KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
+  KEY `seq_region_id_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt

+1	1	469283	1	100	50.3
+2	1	469283	101	200	68.8
+3	1	469283	201	300	32
+4	1	469283	301	400	90.9
+5	1	469283	401	500	88.8
+6	1	469283	501	600	12
+7	2	469283	1	100	50.3
+8	2	469283	101	200	68.8
+9	2	469283	201	300	32
+10	2	469283	301	400	90.9
+11	2	469283	401	500	88.8
+12	2	469283	501	600	12

modules/t/test-genome-DBs/homo_sapiens/core/density_type.sql

+CREATE TABLE `density_type` (
+  `density_type_id` int(11) NOT NULL auto_increment,
+  `analysis_id` int(11) NOT NULL default '0',
+  `block_size` int(11) NOT NULL default '0',
+  `region_features` int(11) NOT NULL default '0',
+  `value_type` enum('sum','ratio') collate latin1_bin NOT NULL default 'sum',
+  PRIMARY KEY  (`density_type_id`),
+  UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+

modules/t/test-genome-DBs/homo_sapiens/core/density_type.txt

+1	1292	100	0	sum
+2	1293	100	0	ratio

modules/t/test-genome-DBs/homo_sapiens/core/ditag.sql

+CREATE TABLE ditag (
+
+       ditag_id INT(10) NOT NULL auto_increment,
+       name VARCHAR(30),
+       type VARCHAR(30),
+       tag_count smallint(6) default 1,
+       sequence TEXT,
+
+       PRIMARY KEY ( ditag_id )
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;

modules/t/test-genome-DBs/homo_sapiens/core/ditag.txt

+3278356	162B08-6	ZZ13	1	GAAGCAAAACACTACAATGGCGGTGCGCTCGACGCGCC
+3278355	198K08-11	ZZ13	1	TTTGATAATTTATTTCAGGCTCTGCGAGAATGAACTC
+3278354	137M14-9	ZZ13	1	GCCTGTTAGATTCACCCCGGTCTCGAGTCTCTCTCTC
+3278353	201K11-2	ZZ13	1	CCTTGAAATTAAGAAGAAGGGCTCGCCGCCGCCGCAC
+3278352	151H04-2	ZZ13	1	GTTCAGTATGGTTTTCAAGAGGGTTAATTGAAAGAG
+3278351	119K09-6	ZZ13	2	TGGAATCTCCATTATTATGAGCGCGCCGCCCCACTCC
+3278350	187N08-1	ZZ13	1	GGAGGTGGATGAGAGGCCAACTCCAGCTCTCTCTCT
+3278349	211G12-2	ZZ13	1	GGGCTGCGATTGCAGCTCACCCTTCGTTAGATAATCA
+3278348	181D04-4	ZZ13	4	TTCTTTCTTTTTTAAAGGGGGTCACGGTCGCCAAACC
+3278347	213E17-4	ZZ13	1	ACATGGGAGACATTTTGCCAAGGCAGCATCAAAAAAC
+3278346	112H10-9	ZZ13	2	AGAGAGAGCTGGAGTTTTGGTAAGAGCATCCTAAGC
+3278345	229D11-1	ZZ13	1	GGCTGGGATAGAGGAGGACGTCTCGAGTCTCTCTCTC
+3278344	235I06-3	ZZ13	1	CGAGAAAAGGAGAGGAGCCTGCTGCCTCCGCCAGAC
+3278343	191F14-10	ZZ13	1	TCCAGCTGCATGAGCAAGGGCCGGGGGCGCGTCAGACC
+3278342	188P19-10	ZZ13	2	ATGGTTATGAGCTGCTCTGCGAGCGCGCGAGTGAGCA
+3278341	224L18-4	ZZ13	1	GTGGCTCCAGGCATCCAGCATAAAATACATGTCTCAA
+3278340	156G19-5	ZZ13	3	GAGAGAGCTGGAGTTTTTACGGAAGCTGCTGCCGCCC
+3278339	189F08-4	ZZ13	1	CACGGCAATTCCTAGGTCCCGAGCGGAATAACAGGCCC
+3278338	134O12-6	ZZ13	1	GGAGACTGCTGGGAGTCCTAAACTCCAGCTCTCTCTCT
+3278337	219H13-10	ZZ13	1	TGCAGCCGCCCATCAAGAATGGGCTCTGGAGGCAGACC