src/hg/makeDb/schema/all.joiner 1.715
1.715 2009/05/20 17:02:17 hiram
Fixup hg19 so it is much cleaner
Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.714
retrieving revision 1.715
diff -b -B -U 4 -r1.714 -r1.715
--- src/hg/makeDb/schema/all.joiner 19 May 2009 21:29:15 -0000 1.714
+++ src/hg/makeDb/schema/all.joiner 20 May 2009 17:02:17 -0000 1.715
@@ -29,8 +29,9 @@
set felCat felCat3
set fr fr1,fr2
set galGal galGal2,galGal3
set gasAcu gasAcu1
+set gorGor gorGor1
set hg hg16,hg17,hg18,hg19
set mm mm7,mm8,mm9
set monDom monDom1,monDom4,monDom5
set ornAna ornAna1
@@ -47,9 +48,9 @@
set tetNig tetNig1
set xenTro xenTro1,xenTro2
# Define all organism/assembly-specific databases.
-set gbd $hg,$mm,$rn,$fr,$ce,$cb,$dm,$dp,$sacCer,$panTro,$galGal,$ci,$danRer,$canFam,$droYak,$droMult,$anoGam,$apiMel,$cioSav,$tetNig,$xenTro,$monDom,$bosTau,$rheMac,$strPur,$felCat,$gasAcu,$oryLat,$equCab,$anoCar,$ornAna,$caePb,$caeRem,$caeJap,$priPac,$ponAbe,$calJac,$cavPor,$petMar,$braFlo,$taeGut
+set gbd $hg,$mm,$rn,$fr,$ce,$cb,$dm,$dp,$sacCer,$panTro,$galGal,$ci,$danRer,$canFam,$droYak,$droMult,$anoGam,$apiMel,$cioSav,$tetNig,$xenTro,$monDom,$bosTau,$rheMac,$strPur,$felCat,$gasAcu,$oryLat,$equCab,$anoCar,$ornAna,$caePb,$caeRem,$caeJap,$priPac,$ponAbe,$calJac,$cavPor,$petMar,$braFlo,$taeGut,$gorGor
# Define organism databases based on whole-genome shotgun projects
# (Assembly based on WGS project contigs accessioned in Genbank)
set wgs $rn,$panTro,$galGal,$canFam,$bosTau,$felCat,$monDom,$tetNig,$fr,$oryLat,$calJac,$cavPor,$taeGut
@@ -85,9 +86,9 @@
databasesChecked $gbd,$otherDb
databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp070202,sp060115,sp051015,sp050415,sp040915,sp040515,sp040315,sp040115,qapushq,mysql-save,hgcentralangie,go070111,go060330,customTracks,customTrash
# Define various non-self chains
-set chainDest Hg16,Hg17,Hg18,Hg19,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CavPor3,PetMar1,BraFlo1,TaeGut1
+set chainDest Hg16,Hg17,Hg18,Hg19,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1
# Define databases that support known genes
set kgDb $hg,$mm,$rn
# Older format (KG 2)
@@ -1040,8 +1041,15 @@
$gbd.netRxBest[].chainId exclude=0
$gbd.net[]NonGap.chainId exclude=0
$gbd.netSynteny[].chainId exclude=0
+identifier chain[${chainDest}]IdNonSplit
+"Link together chain info for chain tables that are not split"
+ hg19.chain[].id
+ hg19.chain[]Link.chainId full
+ hg19.net[].chainId exclude=0
+ hg19.netSynteny[].chainId exclude=0
+
identifier rBestChainPanTro1Id
"Link together reciprocal best chain/net"
hg16.rBestChainPanTro1.id $split
hg16.rBestChainPanTro1Link.chainId $split full
@@ -1833,18 +1841,18 @@
$felCat.ensGene.name dupeOk
$felCat.ensGtp.transcript minCheck=0.99
$felCat.ensPep.name minCheck=0.99
-# Ensembl Links
+# UCSC to Ensembl chrom name translation
identifier ensemblLinkId external=Ensembl dependency
"Ensembl Links from hgTracks"
- $hg.chromInfo.chrom
- $hg.ucscToEnsembl.ucsc
+ hg18,hg19.chromInfo.chrom
+ hg18,hg19.ucscToEnsembl.ucsc
-identifier ucscLinkId external=Ensembl dependency
-"Ensembl Mappings from hgTracks"
- $hg.ucscToEnsembl.ensembl
- $hg.ensemblLift.chrom
+identifier ucscToEnsembl external=Ensembl dependency
+"UCSC to Ensembl chrom name translation"
+ hg18,hg19.ucscToEnsembl.ensembl
+ hg18,hg19.ensemblLift.chrom
# Ensembl EST
identifier ensemblEstTranscriptId external=Ensembl dependency
@@ -2941,8 +2949,53 @@
pep%Dist
tablesIgnored hg19
gold
+ bacEndPairsBad
+ multizMHCSummary
+ netSyn_mann_hap4
+ net_dbb_hap3
+ net_apd_hap1
+ net_ssto_hap7
+ net_qbl_hap6
+ net_mcf_hap5
+ net_mann_hap4
+ net_haplotypes
+ net_cox_hap2
+ net_chr4_ctg9_hap1
+ net_chr17_ctg5_hap1
+ netVenter1
+ netSyn_ssto_hap7
+ netSyn_qbl_hap
+ netSyn_qbl_hap6
+ netSyn_mcf_hap5
+ netSyn_apd_hap1
+ netSyn_cox_hap2
+ netSyn_dbb_hap3
+ chain_ssto_hap7
+ chain_ssto_hap7Link
+ hapRegions
+ multizMHC
+ chain_mcf_hap5Link
+ chain_qbl_hap6
+ chain_qbl_hap6Link
+ chain_haplotypesLink
+ chain_mann_hap4
+ chain_mann_hap4Link
+ chain_mcf_hap5
+ chain_chr4_ctg9_hap1
+ chain_chr4_ctg9_hap1Link
+ chain_cox_hap2
+ chain_cox_hap2Link
+ chain_dbb_hap3
+ chain_dbb_hap3Link
+ chainVenter1
+ chainVenter1Link
+ chain_apd_hap1
+ chain_apd_hap1Link
+ chain_chr17_ctg5_hap1
+ chain_chr17_ctg5_hap1Link
+ chain_haplotypes
tablesIgnored $calJac
gold