src/hg/makeDb/schema/all.joiner 1.776
1.776 2010/03/31 16:29:04 hiram
adding susScr2 ailMel1 and fixing up chain checks
Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.775
retrieving revision 1.776
diff -b -B -U 4 -r1.775 -r1.776
--- src/hg/makeDb/schema/all.joiner 25 Mar 2010 18:28:56 -0000 1.775
+++ src/hg/makeDb/schema/all.joiner 31 Mar 2010 16:29:04 -0000 1.776
@@ -1,8 +1,9 @@
# This contains linkage information between various fields
# in various databases.
# Define databases used for various organisms
+set ailMel ailMel1
set anoCar anoCar1
set anoGam anoGam1
set apiMel apiMel1,apiMel2
set aplCal aplCal1
@@ -26,9 +27,9 @@
set droMult droAna1,droAna2,droMoj1,droMoj2,droVir1,droVir2,droEre1,droSim1,droGri1,droPer1,droSec1,droWil1
set droVir droVir1,droVir2
set droYak droYak1,droYak2
set equCab equCab1,equCab2
-set felCat felCat3
+set felCat felCat3,felCatV17e
set fr fr1,fr2
set galGal galGal2,galGal3
set gasAcu gasAcu1
set gorGor gorGor1
@@ -45,22 +46,23 @@
set priPac priPac1
set rheMac rheMac2
set rn rn3,rn4
set sacCer sacCer1,sacCer2
+set susScr susScr2
set strPur strPur1,strPur2
set taeGut taeGut1
set tetNig tetNig1,tetNig2
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,$gasAcu,$oryCun,$oryLat,$equCab,$anoCar,$ornAna,$caePb,$caeRem,$caeJap,$priPac,$ponAbe,$calJac,$cavPor,$petMar,$braFlo,$taeGut,$gorGor,$aplCal,$loxAfr,$aplCal
+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,$gasAcu,$oryCun,$oryLat,$equCab,$anoCar,$ornAna,$caePb,$caeRem,$caeJap,$priPac,$ponAbe,$calJac,$cavPor,$petMar,$braFlo,$taeGut,$gorGor,$aplCal,$loxAfr,$aplCal,$susScr,$ailMel
# 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,$fr,$oryCun,$oryLat,$calJac,$cavPor,$taeGut,$aplCal
# Define organism databases for which we build a xenoRefGene track:
-set xrg $panTro,$galGal,$ci,$canFam,$dp,$droYak,$droMult,$bosTau,$rn,$hg,$rheMac,$monDom,$felCat,$oryCun,$oryLat,$anoCar,$caePb,$caeRem,$caeJap,$cb,$mm,$priPac,$strPur,$ponAbe,$calJac,$petMar,$braFlo,$ce,$taeGut,danRer6,$aplCal
+set xrg $panTro,$galGal,$ci,$canFam,$dp,$droYak,$droMult,$bosTau,$rn,$hg,$rheMac,$monDom,$felCat,$oryCun,$oryLat,$anoCar,$caePb,$caeRem,$caeJap,$cb,$mm,$priPac,$strPur,$ponAbe,$calJac,$petMar,$braFlo,$ce,$taeGut,danRer6,$aplCal,$ailMel,$loxAfr
# Define organism databases for which we build a SNP track:
set snpDb130 hg18
set snpDb129 hg18
@@ -82,19 +84,17 @@
set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3
# Define transMap databases
# transMapDb not public: dasNov1,echTel1,loxAfr1,oryCun1,otoGar1,loxAfr3
-set transMapDb anoCar1,bosTau4,calJac1,canFam2,cavPor3,danRer5,danRer6,equCab2,felCat3,fr2,galGal3,gasAcu1,hg18,hg19,mm9,monDom4,monDom5,ornAna1,oryCun2,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,tetNig2,xenTro2
+set transMapDb anoCar1,bosTau4,calJac1,canFam2,cavPor3,danRer5,danRer6,equCab2,felCat3,fr2,galGal3,gasAcu1,hg18,hg19,mm9,monDom4,monDom5,ornAna1,oryCun2,oryLat2,panTro2,petMar1,ponAbe2,rheMac2,rn4,taeGut1,tetNig1,tetNig2,xenTro2,loxAfr3
# Set up list of databases we ignore and those we check. Program
# will complain about other databases.
databasesChecked $gbd,$otherDb
databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp090821,sp080707,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,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,TetNig2,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,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr3
-
-set nonSplitChains hg19,$tetNig,oryCun2
+set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,TetNig2,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,CalJac3,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr2,LoxAfr3,SusScr1,SusScr2,AilMel1,FelCatV17e,CanFamPoodle1,ChoHof1,DasNov2,DipOrd1,EchTel1,EriEur1,MacEug1,MyoLuc1,OchPri2,OryCun1,OryCun2,ProCap1,PteVam1,SorAra1,SpeTri1,TupBel1,TurTru1,VicPac1
# Define databases that support known genes
set kgDb $hg,$mm,$rn
# Older format (KG 2)
@@ -1073,21 +1073,16 @@
identifier chain[${chainDest}]Id
"Link together chain info"
$gbd.chain[].id $split
+ $gbd.chain[].id
$gbd.chain[]Link.chainId $split full
+ $gbd.chain[]Link.chainId full
$gbd.net[].chainId exclude=0
$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"
- $nonSplitChains.chain[].id
- $nonSplitChains.chain[]Link.chainId full
- $nonSplitChains.net[].chainId exclude=0
- $nonSplitChains.netSynteny[].chainId exclude=0
-
identifier rBestChainPanTro1Id
"Link together reciprocal best chain/net"
hg16.rBestChainPanTro1.id $split
hg16.rBestChainPanTro1Link.chainId $split full
@@ -1178,8 +1173,9 @@
$gbd,!sacCer2,!caeJap1.intronEst.qName $split
sacCer2.est.qName splitPrefix=%\_ full
sacCer2.intronEst.qName splitPrefix=%\_
caeJap1.intronEst.qName
+ ailMel1.intronEst.qName
$gbd.estOrientInfo.name full
identifier nativeEstAccessionNonSplit typeOf=estAccession
"Genbank Native (same organism as database) EST accession"
@@ -3120,11 +3116,8 @@
flyreg2
tablesIgnored $loxAfr
gold
- chainHg19
- chainHg19Link
- xenoRefFlat
tablesIgnored $equCab
chr%_gold
@@ -3518,4 +3511,12 @@
tablesIgnored oryCun2
ctgPos2
gold
intronEst
+
+tablesIgnored susScr2
+ bosTau4ChainPileUp
+ gold
+ ctgPos2
+
+tablesIgnored ailMel1
+ gold