WashU Epigenome Browser

mock	images/mock.png	Mock data set	\N	Just a mock data set...

AGPv2_5a	Maize genes	\N	2	0	1	http://www.maizesequence.org/Zea_mays/Gene?db=core;gene=

AGPv2_5apromoter	promoters (RefSeq genes)	AGPv2_5a	2	0	0	\N

AGPv2_5autr3	3' UTRs (RefSeq genes)	AGPv2_5a	2	0	0	\N

AGPv2_5autr5	5' UTRs (RefSeq genes)	AGPv2_5a	2	0	0	\N

AGPv2_5aexons	exons (RefSeq genes)	AGPv2_5a	2	0	0	\N

AGPv2_5aintrons	introns (RefSeq genes)	AGPv2_5a	2	0	0	\N

refGene	RefSeq genes	\N	2	0	1	http://www.ncbi.nlm.nih.gov/gene/?term=

refGenepromoter	promoters (RefSeq genes)	refGene	2	0	0	\N

refGeneutr3	3' UTRs (RefSeq genes)	refGene	2	0	0	\N

refGeneutr5	5' UTRs (RefSeq genes)	refGene	2	0	0	\N

refGeneexons	exons (RefSeq genes)	refGene	2	0	0	\N

refGeneintrons	introns (RefSeq genes)	refGene	2	0	0	\N

MTECrepeats	All repeats	\N	4	0	0	\N

LINE	LINE	\N	4	0	0	\N

LINE [RIL] L1	LINE [RIL] L1	LINE	4	0	0	\N

LINE [RIX] Unknown	LINE [RIX] Unknown	LINE	4	0	0	\N

LTR	LTR	\N	4	0	0	\N

LTR [RLC] Copia	LTR [RLC] Copia	LTR	4	0	0	\N

LTR [RLG] Gypsy	LTR [RLG] Gypsy	LTR	4	0	0	\N

LTR [RLX] Unknown	LTR [RLX] Unknown	LTR	4	0	0	\N

TIR	TIR	\N	4	0	0	\N

TIR [DTA] hAT	TIR [DTA] hAT	TIR	4	0	0	\N

TIR [DTC] CACTA	TIR [DTC] CACTA	TIR	4	0	0	\N

TIR [DTH] Pif-Harbinger	TIR [DTH] Pif-Harbinger	TIR	4	0	0	\N

TIR [DTM] Mutator	TIR [DTM] Mutator	TIR	4	0	0	\N

TIR [DTT] Tc1-Mariner	TIR [DTT] Tc1-Mariner	TIR	4	0	0	\N

gc5Base	GC percent	\N	5	14	0	\N

-- ------------------------

--                       --

--      AGPv2heatmap     --

--                       --

-- ------------------------

drop table if exists config;

create table config (

  bbiPath text not null,

  seqPath text null,

  defaultTracks text not null,

  defaultMdcategory varchar(255) not null,

  defaultGenelist text not null,

  defaultCustomtracks text not null,

  defaultPosition varchar(255) not null,

  defaultDataset varchar(255) not null,

  defaultDecor text null,

  defaultScaffold text not null,

  ideogram_wiggle1 varchar(255) null,

  ideogram_wiggle2 varchar(255) null,

  hasGene boolean not null,

  allowJuxtaposition boolean not null,

  keggSpeciesCode varchar(255) null,

  information text not null,

  runmode tinyint not null,

  initmatplot boolean not null

);

insert into config values(

"/srv/epgg/data/data/subtleKnife/b73_AGPv2/",

"/srv/epgg/data/data/subtleKnife/seq/AGPv2.gz",

"mock1,mock2,mock3,mock4,mock5,mock6,mock7,mock8,mock9,mock10,mock11,mock12,mock13,mock14,mock15,mock16,mock17,mock18,mock19,mock20", 

"Sample,mock term",

"gst23\\ngst40\\ngst8\\ngst30\\ngst14\\ngst11\\ngst12\\ngst16\\ngst7\\ngst19\\ngst41\\ngst9\\ngst35\\ngst24\\ngst31\\nBz2",

"3,http://vizhub.wustl.edu/hubSample/AGPv2/rand4.gz,1,http://vizhub.wustl.edu/hubSample/AGPv2/sample.gz,100,http://vizhub.wustl.edu/hubSample/AGPv2/hub.txt",

"chr1,11500000,chr1,12000000",

"mock",

"refGene,AGPv2_5a",

"chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10",

\N,\N,

true,

true,

"zma",

"Strain|B73|Assembly version|AGPv2|Sequence source|<a href=http://www.maizesequence.org target=_blank>maizesequence.org</a>|Date parsed|May 19, 2012|Chromosomes|13|Contigs|0|Total bases|3,232,254,451|Logo art|<a href=http://en.wikipedia.org/wiki/File:Zea_mays_-_K%C3%B6hler%E2%80%93s_Medizinal-Pflanzen-283.jpg target=_blank>link</a>",

0,

false

);

-- grouping types on genomic features

-- table name defined in macro: TBN_GF_GRP

drop table if exists gfGrouping;

create table gfGrouping (

  id TINYINT not null primary key,

  name char(50) not null

);

insert into gfGrouping values (2, "Genes");

insert into gfGrouping values (4, "TE Consortium repeats");

insert into gfGrouping values (5, "Others");

drop table if exists decorInfo;

create table decorInfo (

  name char(50) not null primary key,

  printname char(100) not null,

  parent char(50) null,

  grp tinyint not null,

  fileType tinyint not null,

  hasStruct tinyint null,

  queryUrl varchar(255) null

);

load data local infile 'decorInfo' into table decorInfo;

/*

insert into decorInfo values('AGPv2_5a','Maize genes',\N,2,0,1,'http://www.maizesequence.org/Zea_mays/Gene?db=core;gene=');

insert into decorInfo values('AGPv2_5apromoter','promoters (RefSeq genes)','AGPv2_5a',2,0,0,\N);

insert into decorInfo values('AGPv2_5autr3',"3' UTRs (RefSeq genes)",'AGPv2_5a',2,0,0,\N);

insert into decorInfo values('AGPv2_5autr5',"5' UTRs (RefSeq genes)",'AGPv2_5a',2,0,0,\N);

insert into decorInfo values('AGPv2_5aexons','exons (RefSeq genes)','AGPv2_5a',2,0,0,\N);

insert into decorInfo values('AGPv2_5aintrons','introns (RefSeq genes)','AGPv2_5a',2,0,0,\N);

insert into decorInfo values('refGene','RefSeq genes',\N,2,0,1,'http://www.ncbi.nlm.nih.gov/gene/?term=');

insert into decorInfo values('refGenepromoter','promoters (RefSeq genes)','refGene',2,0,0,\N);

insert into decorInfo values('refGeneutr3',"3' UTRs (RefSeq genes)",'refGene',2,0,0,\N);

insert into decorInfo values('refGeneutr5',"5' UTRs (RefSeq genes)",'refGene',2,0,0,\N);

insert into decorInfo values('refGeneexons','exons (RefSeq genes)','refGene',2,0,0,\N);

insert into decorInfo values('refGeneintrons','introns (RefSeq genes)','refGene',2,0,0,\N);

insert into decorInfo values ('MTECrepeats','All repeats',\N, 4, 0, 0,\N);

insert into decorInfo values ('LINE','LINE',\N, 4, 0, 0,\N);

insert into decorInfo values ('LINE [RIL] L1','LINE [RIL] L1','LINE', 4, 0, 0,\N);

insert into decorInfo values ('LINE [RIX] Unknown','LINE [RIX] Unknown','LINE', 4, 0, 0,\N);

insert into decorInfo values ('LTR','LTR',\N, 4, 0, 0,\N);

insert into decorInfo values ('LTR [RLC] Copia','LTR [RLC] Copia','LTR', 4, 0, 0,\N);

insert into decorInfo values ('LTR [RLG] Gypsy','LTR [RLG] Gypsy','LTR', 4, 0, 0,\N);

insert into decorInfo values ('LTR [RLX] Unknown','LTR [RLX] Unknown','LTR', 4, 0, 0,\N);

insert into decorInfo values ('TIR','TIR',\N, 4, 0, 0,\N);

insert into decorInfo values ('TIR [DTA] hAT','TIR [DTA] hAT', 'TIR', 4, 0, 0,\N);

insert into decorInfo values ('TIR [DTC] CACTA','TIR [DTC] CACTA', 'TIR', 4, 0, 0,\N);

insert into decorInfo values ('TIR [DTH] Pif-Harbinger','TIR [DTH] Pif-Harbinger', 'TIR', 4, 0, 0,\N);

insert into decorInfo values ('TIR [DTM] Mutator','TIR [DTM] Mutator', 'TIR', 4, 0, 0,\N);

insert into decorInfo values ('TIR [DTT] Tc1-Mariner','TIR [DTT] Tc1-Mariner', 'TIR', 4, 0, 0,\N);

insert into decorInfo values ('gc5Base','GC percent', \N,5, 8, 0,\N);

*/

drop table if exists track2Label;

create table track2Label (

  name varchar(255) not null primary key,

  label text null

);

load data local infile 'track2Label' into table track2Label;

drop table if exists track2ProcessInfo;

create table track2ProcessInfo (

  name varchar(255) not null primary key,

  detail text null

);

load data local infile 'track2ProcessInfo' into table track2ProcessInfo;

drop table if exists track2BamInfo;

create table track2BamInfo (

  name varchar(255) not null,

  bamfile varchar(255) not null,

  bamfilelabel varchar(255) not null

);

load data local infile "track2BamInfo" into table track2BamInfo;

drop table if exists track2Detail;

create table track2Detail (

  name varchar(255) not null primary key,

  detail text null

);

load data local infile 'track2Detail' into table track2Detail;

drop table if exists track2GEO;

create table track2GEO (

  name varchar(255) not null primary key,

  geo char(20) not null

);

load data local infile 'track2GEO' into table track2GEO;

drop table if exists track2VersionInfo;

create table track2VersionInfo (

  name varchar(255) not null primary key,

  info varchar(255) not null

);

load data local infile 'track2VersionInfo' into table track2VersionInfo;

-- new trackDetail end here

drop table if exists track2Annotation;

create table track2Annotation (

  name varchar(255) not null primary key,

  attridx varchar(255) not null

);

load data local infile "track2Annotation" into table track2Annotation;

drop table if exists track2Ft;

create table track2Ft (

  name varchar(255) not null primary key,

  ft tinyint not null

);

load data local infile "track2Ft" into table track2Ft;

drop table if exists track2Style;

create table track2Style (

  name varchar(255) not null primary key,

  style text not null

);

load data local infile "track2Style" into table track2Style;

drop table if exists track2Regions;

create table track2Regions (

  name varchar(255) not null primary key,

    regionname varchar(255) not null,

	  regions text not null

	   );

drop table if exists metadataVocabulary;

create table metadataVocabulary (

  child varchar(255) not null,

  parent varchar(255) not null

);

load data local infile "metadataVocabulary" into table metadataVocabulary;

drop table if exists trackAttr2idx;

create table trackAttr2idx (

  idx varchar(255) not null primary key,

  attr varchar(255) not null,

  note varchar(255) null,

  description text null

);

load data local infile "trackAttr2idx" into table trackAttr2idx;

drop table if exists tempURL;

create table tempURL (

  session varchar(100) not null,

  offset INT unsigned not null,

  urlpiece text not null

);

drop table if exists dataset;

create table dataset (

  tablename varchar(255) not null,

  logo varchar(255) null,

  name varchar(255) not null,

  url varchar(255) null,

  description text not null

);

load data local infile "dataset" into table dataset;

drop table if exists mock;

create table mock (

  tkname varchar(255) not null

);

load data local infile "mock" into table mock;

drop table if exists scaffoldInfo;

create table scaffoldInfo (

  parent varchar(255) not null,

  child varchar(255) not null,

  childLength int unsigned not null

  );

load data local infile "scaffoldInfo" into table scaffoldInfo;

drop table if exists cytoband;

create table cytoband (

  id int null auto_increment primary key,

  chrom char(20) not null,

  start int not null,

  stop int not null,

  name char(20) not null,

  colorIdx int not null

);

load data local infile "cytoband" into table cytoband;

/*

DROP TABLE IF EXISTS `rmsk`;

CREATE TABLE `rmsk` (

  `bin` smallint(5) unsigned NOT NULL default '0',

  `swScore` int(10) unsigned NOT NULL default '0',

  `milliDiv` int(10) unsigned NOT NULL default '0',

  `milliDel` int(10) unsigned NOT NULL default '0',

  `milliIns` int(10) unsigned NOT NULL default '0',

  `genoName` varchar(255) NOT NULL default '',

  `genoStart` int(10) unsigned NOT NULL default '0',

  `genoEnd` int(10) unsigned NOT NULL default '0',

  `genoLeft` int(11) NOT NULL default '0',

  `strand` char(1) NOT NULL default '',

  `repName` varchar(255) NOT NULL default '',

  `repClass` varchar(255) NOT NULL default '',

  `repFamily` varchar(255) NOT NULL default '',

  `repStart` int(11) NOT NULL default '0',

  `repEnd` int(11) NOT NULL default '0',

  `repLeft` int(11) NOT NULL default '0',

  `id` char(1) NOT NULL default '',

  KEY `genoName` (`genoName`(14),`bin`)

);

load data local infile 'rmsk.txt' into table rmsk;

*/

mock term	Sample

401	mock term

402	mock term

403	mock term

404	mock term

405	mock term

406	mock term

407	mock term

408	mock term

409	mock term

410	mock term

411	mock term

412	mock term

413	mock term

414	mock term

415	mock term

416	mock term

417	mock term

418	mock term

419	mock term

420	mock term

mock1

mock2

mock3

mock4

mock5

mock6

mock7

mock8

mock9

mock10

mock11

mock12

mock13

mock14

mock15

mock16

mock17

mock18

mock19

mock20

ROOT	chromosome	0

chromosome	chr5	217872852

chromosome	chr7	176764762

chromosome	chrMt	569630

chromosome	chr6	169174353

chromosome	chr10	150189435

chromosome	chr9	156750706

chromosome	chr1	301354135

chromosome	chr4	241473504

chromosome	chrUNKNOWN	7140151

chromosome	chr8	175793759

chromosome	chrPt	140384

chromosome	chr3	232140174

chromosome	chr2	237068873

mock1	401

mock2	402

mock3	403

mock4	404

mock5	405

mock6	406

mock7	407

mock8	408

mock9	409

mock10	410

mock11	411

mock12	412

mock13	413

mock14	414

mock15	415

mock16	416

mock17	417

mock18	418

mock19	419

mock20	420

mock20	\N

mock19	\N

mock18	\N

mock13	\N

mock12	\N

mock11	\N

mock10	\N

mock17	\N

mock16	\N

mock15	\N

mock14	\N

mock9	\N

mock8	\N

mock3	\N

mock2	\N

mock1	\N

mock7	\N

mock6	\N

mock5	\N

mock4	\N

mock1	2

mock2	2

mock3	2

mock4	2

mock5	2

mock6	2

mock7	2

mock8	2

mock9	2

mock10	2

mock11	2

mock12	2

mock13	2

mock14	2

mock15	2

mock16	2

mock17	2

mock18	2

mock19	2

mock20	2

mock20	mock20

mock19	mock19

mock18	mock18

mock13	mock13

mock12	mock12

mock11	mock11

mock10	mock10

mock17	mock17

mock16	mock16

mock15	mock15

mock14	mock14

mock9	mock9

mock8	mock8

mock3	mock3

mock2	mock2

mock1	mock1

mock7	mock7

mock6	mock6

mock5	mock5

mock4	mock4

AGPv2_5a	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

AGPv2_5aexons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

AGPv2_5aintrons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

AGPv2_5apromoter	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

AGPv2_5autr3	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

AGPv2_5autr5	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LINE	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LINE [RIL] L1	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LINE [RIX] Unknown	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LTR	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LTR [RLC] Copia	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LTR [RLG] Gypsy	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

LTR [RLX] Unknown	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

MTECrepeats	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

refGene	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

refGeneexons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

refGeneintrons	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

refGenepromoter	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

refGeneutr3	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

refGeneutr5	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

TIR	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

TIR [DTA] hAT	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

TIR [DTC] CACTA	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

TIR [DTH] Pif-Harbinger	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

TIR [DTM] Mutator	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

TIR [DTT] Tc1-Mariner	'textcolor':'rgb(0,0,0)','fontsize':'8pt','fontfamily':'sans-serif','fontbold':false,'bedcolor':'rgb(0,77,153)'

gc5Base	\N

401	1	mock	mock 1

402	2	mock	mock 2

403	3	mock	mock 3

404	4	mock	mock 4

405	5	mock	mock 5

406	6	mock	mock 6

407	7	mock	mock 7

408	8	mock	mock 8

409	9	mock	mock 9

410	10	mock	mock 10

411	11	mock	mock 11

412	12	mock	mock 12

413	13	mock	mock 13

414	14	mock	mock 14

415	15	mock	mock 15

416	16	mock	mock 16

417	17	mock	mock 17

418	18	mock	mock 18

419	19	mock	mock 19

420	20	mock	mock 20

print 'ROOT\tchromosome\t0\nROOT\tcontig\t0'

fout=open('longstr','w')

with open('chromlen') as fin:

	for line in fin:

		lst=line.rstrip().split('\t')

		if lst[0].startswith('Scaffold') or lst[0].startswith('scaffold'):

			print 'chromosome\t{0}\t{1}'.format(lst[0],lst[1])

			fout.write(lst[0]+',')

		else:

			print 'contig\t{0}\t{1}'.format(lst[0],lst[1])

fout.write('\n')

fout.close()

# sort -k2nr

scaffold217	3188626

scaffold174	2527684

scaffold121	2456259

scaffold751	2448386

scaffold74	2050049

scaffold221	2027244

scaffold868	1815522

scaffold83	1772090

scaffold380	1770217

scaffold426	1729492

scaffold895	1718955

scaffold449	1687578

scaffold91	1677483

scaffold67	1646982

scaffold735	1626371

scaffold88	1615178

scaffold266	1606235

scaffold185	1584263

scaffold112	1548205

scaffold682	1492960

scaffold36	1484530

scaffold890	1460389

scaffold257	1452135

scaffold24	1417469

scaffold155	1397119

scaffold387	1383393

scaffold549	1379847

scaffold35	1378841

scaffold249	1367122

scaffold122	1363751

scaffold1195	1358118

scaffold455	1352435

scaffold343	1346714

scaffold440	1345499

scaffold443	1301167

scaffold213	1286099

scaffold150	1278466

scaffold314	1270913

scaffold160	1245850

scaffold22	1239070

scaffold16	1236715

scaffold7	1234265

scaffold674	1222776

scaffold514	1221598

scaffold531	1208664

scaffold85	1202131

scaffold582	1195895

scaffold432	1188868

scaffold128	1185424

scaffold816	1183837

scaffold371	1181502

scaffold54	1171839

scaffold163	1171795

scaffold484	1156222

scaffold53	1147598

scaffold984	1144119

scaffold33	1132667

scaffold899	1132184

scaffold207	1125759

scaffold253	1113591

scaffold481	1111314

scaffold61	1110436

scaffold57	1108522

scaffold555	1106060

scaffold720	1103897

scaffold497	1085415

scaffold219	1082942

scaffold81	1069547

scaffold492	1068411

scaffold866	1063658

scaffold451	1062816

scaffold269	1049116

scaffold410	1048880

scaffold659	1038070

scaffold224	1036736

scaffold261	1032209

scaffold1376	1027989

scaffold206	1026360

scaffold247	1025490

scaffold141	1023219

scaffold444	1013279

scaffold4	1008686

scaffold123	1007854

scaffold576	1007760

scaffold968	1007679

scaffold31	1002484

scaffold703	1000728

scaffold181	994954

scaffold186	992989

scaffold460	982512

scaffold37	971384

scaffold195	969349

scaffold510	968124

scaffold260	966697

scaffold477	953893

scaffold469	943810

scaffold153	941857

scaffold289	933511

scaffold452	932170

scaffold1055	925783

scaffold140	925777

scaffold84	923568

scaffold609	923298

scaffold448	917689

scaffold544	915346

scaffold1306	910419

scaffold161	909092

scaffold382	908460

scaffold340	905765

scaffold49	894794

scaffold784	893950

scaffold591	893091

scaffold82	886116

scaffold1179	882481

scaffold420	882049

scaffold535	875384

scaffold379	874727

scaffold593	870598

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