64ca0b57ba8357a2a2f402a182eda252d6cbfb70
hiram
  Wed Jul 3 15:45:28 2019 -0700
adding rules for rheMac10 and regenRn0 refs #23771 #21578

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index fdb28af..2d5692d 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -110,34 +110,34 @@
 set oxyTri oxyTri2
 set panPan panPan1,panPan2
 set panManBai panManBai1
 set panTro panTro1,panTro2,panTro3,panTro4,panTro5,panTro6
 set papAnu papAnu2,papAnu3,papAnu4
 set papHam papHam1
 set petMar petMar1,petMar2,petMar3
 set pelSin pelSin1
 set perMan perManBai1
 set poeFor poeFor1
 set ponAbe ponAbe2,ponAbe3
 set priPac priPac1,priPac2,priPac3
 set proCap proCap1
 set proCoq proCoq1
 set pteVam pteVam1
-set rheMac rheMac2,rheMac3,rheMac8
+set rheMac rheMac2,rheMac3,rheMac8,rheMac10
 set rhiBie rhiBie1
 set rhiRox rhiRox1
-set rn rn3,rn4,rn5,rn6
+set rn rn3,rn4,rn5,rn6,regenRn0
 set rouAeg rouAeg1
 set sacCer sacCer1,sacCer2,sacCer3
 set saiBol saiBol1
 set sarHar sarHar1
 set sorAra sorAra1,sorAra2
 set speTri speTri1,speTri2
 set susScr susScr1,susScr2,susScr3,susScr11
 set staAur staAur1,staAur2
 set strPur strPur1,strPur2
 set tarSyr tarSyr1,tarSyr2
 set taeGut taeGut1,taeGut2
 set tetNig tetNig1,tetNig2
 set thaSir thaSir1
 set triMan triMan1
 set tupBel tupBel1
@@ -198,31 +198,31 @@
 set proteinDb proteins070202,proteins060115,proteins050415,proteins051015,proteins050415,proteins050315,proteins050201,proteins041115,proteins040515,proteins040315,proteins0111,proteins0305,proteins031112,proteins040115,proteins0405,proteins070403,proteins072003,proteins092903,proteins1129
 
 # Define zoo databases (currently not checked)
 set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3
 
 # Define ucscRetro databases
 set ucscRetroDb hg19,hg38,mm9,mm10
 
 # Set up list of databases we ignore and those we check.  Program
 # will complain about other databases.
 
 databasesChecked $gbd,$otherDb,hgFixed
 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,10Kgenomes,BRfoo,abc,andy,bioCyc070327,bioCyc090623,bioCyc100514,bosTau3Old,ccds,ccds20080404,ccdsNew,ccds_before,ctd,ctd021508,ctdOld,dark,elegansWS176,encpipeline_aamp,encpipeline_beta,encpipeline_galt,encpipeline_kate,encpipeline_prod,encpipeline_test,entrez,euaGli13,eutHer13,fakeDataE0,fanKgTemp,fanKgTemp2,fanTest,fanTest2,gencode,germlineVar_hg18,go040501,go041115,go050521,go050726,go060211,go061219,go080130,goJill,hg15test,hg18kg11,hg18snp130,hg18test,hg19Haps,hg19Patch10,hg19Patch13,hg19Patch9,hg19Patch5,hg19Patch2,hg19Patch2i,hg38Patch2,hg38Patch3,hg38Patch5,hg38Patch6,hg38Patch7,hg38Patch9,hg38Patch11,hg19snp131,hg19snp132,hg19snp134,hg19snp135,hg19snp137,hg19snp138,hg19snp141,hg38snp141,hg19snp142,hg38snp142,hg19snp144,hg38snp144,hg19snp146,hg38snp146,hg19snp147,hg38snp147,hg19snp149,hg38snp149,hg19snp150,hg38snp150,hg19snp151,hg38snp151,mm10snp138,canFam3snp139,bosTau7snp138,bosTau8snp148,susScr3snp138,galGal4snp138,hgcentralgsid,hgcentralrhead,hgcentraltest2,hgcentraltestangie,hiv1,hivgne8,homIni13,homIni14,homIni20,homNea0,homPan20,influenza,information_schema,ismb2004,jkFoo,jorgetest,kgHg17FTemp,kgHg18ATemp,kgMm8ATemp,kgRn3DTemp,markd,markdCcds,markdMGC,membership,metaData_vsmalladi,metadata_krish,mikep,mm9Temp,mm10snp137,mmtv,nonAfr13,oldChoHof1,panTro2snp127,pathway,petMar0,pongo,proteins080707,proteins090821,qa,rah,reactome,rn4UCGenes,rn4snp130,snpCompare,snpFixed,sp100331,sp101005,t18,testMePrivl,tmpBioCychg18,tmpFoo12,tmpUcscGeneshg19,treeFam,uf,ug,vega33,vega40,visiGeneOld,visiGeneXml
 
 # Define various non-self chains
-set chainDest AilMel1,AmbMex1,AncCey1,AnoCar1,AnoCar2,AnoGam1,ApiMel1,ApiMel2,ApiMel3,ApiMel4,AplCal1,AscSuu1,BosTau1,BosTau2,BosTau3,BosTau4,BosTau6,BosTau7,BosTau8,BosTau9,BraFlo1,BraFlo2,BruMal1,BruMal2,BurXyl1,CaeAng1,CaeAng2,CaeJap1,CaeJap3,CaeJap4,CaePb1,CaePb2,CaePb3,CaeRem2,CaeRem3,CaeRem4,CaeSp111,CaeSp51,CalJac1,CalJac3,CalMil1,CanFam1,CanFam2,CanFam3,CanFamPoodle1,CavPor3,Cb1,Cb3,Cb4,Ce2,Ce4,Ce6,Ce9,Ce10,Ce11,ChlSab1,ChlSab2,ChoHof1,ChrPic2,Ci1,Ci2,CioSav2,ColAng1,CriGri1,CriGriChoV1,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,DanRer7,DanRer10,DasNov2,DasNov3,DipOrd1,DirImm1,Dm1,Dm2,Dm3,Dm6,Dp1,Dp2,Dp3,Dp4,DroAlb1,DroAna1,DroAna2,DroAna3,DroBia2,DroBip2,DroEle2,DroEre1,DroEre2,DroEug2,DroFic2,DroGri1,DroGri2,DroKik2,DroMir2,DroMoj1,DroMoj2,DroMoj3,DroPer1,DroPse3,DroRho2,DroSec1,DroSim1,DroSuz1,DroTak2,DroVir1,DroVir2,DroVir3,DroWil1,DroWil2,DroYak1,DroYak2,DroYak3,EchTel1,EquCab1,EquCab2,EquCab3,EriEur1,EriEur2,FalPer1,FelCat3,FelCat4,FelCat5,FelCat8,FelCat9,Fr1,Fr2,Fr3,GadMor1,GalGal2,GalGal3,GalGal4,GalGal5,GalGal6,GalVar1,GasAcu1,GeoFor1,GorGor1,GorGor2,GorGor3,GorGor4,GorGor5,HaeCon1,HaeCon2,HetBac1,HetGla1,HetGla2,Hg16,Hg17,Hg18,Hg19,Hg19Patch2,Hg19Patch5,Hg19Patch9,Hg19Patch10,Hg19Patch13,Hg38Patch2,Hg38Patch3,Hg38Patch5,Hg38Patch6,Hg38Patch7,Hg38Patch9,Hg38Patch11,Hg38,LatCha1,LepWed1,LoaLoa1,LoxAfr2,LoxAfr3,MacEug1,MacEug2,MacFas5,MarVir1,MayZeb1,MelGal1,MelGal5,MelHap1,MelInc1,MelInc2,MelUnd1,MesAur1,MicMur1,MicMur2,MicMur3,MicOch1,Mm5,Mm6,Mm7,Mm8,Mm9,Mm10,Mm10Patch1,Mm10Patch4,MonDom1,MonDom2,MonDom4,MonDom5,MusDom2,MyoLuc1,MyoLuc2,NanPar1,NasLar1,NecAme1,NomLeu1,NomLeu2,NomLeu3,OchPri2,OncVol1,OreNil1,OreNil2,OreNil3,OrnAna1,OrnAna2,OryCun1,OryCun2,OryLat1,OryLat2,OtoGar1,OtoGar3,OviAri1,OviAri3,OviAri4,PanPan1,PanRed1,PanTro1,PanTro2,PanTro3,PanTro4,PanTro5,PanTro6,PapAnu2,PapAnu3,PapHam1,PelSin1,PetMar1,PetMar2,PetMar3,PonAbe2,PonAbe3,PriExs1,PriPac1,PriPac2,PriPac3,ProCap1,ProCoq1,PteVam1,RheMac1,RheMac2,RheMac3,RheMac8,RhiRox1,Rn3,Rn4,Rn5,Rn6,SaiBol1,SorAra1,SpeTri1,SpeTri2,StrRat1,StrRat2,StrPur1,StrPur2,SusScr1,SusScr2,SusScr3,SusScr11,TaeGut1,TaeGut2,TarSyr1,TarSyr2,TetNig1,TetNig2,TriCas2,TriMan1,TriSpi1,TriSui1,TupBel1,TurTle1,TurTru1,TurTru2,VicPac1,VicPac2,XenLae2,XenTro1,XenTro2,XenTro3,XenTro7,XenTro9
+set chainDest AilMel1,AmbMex1,AncCey1,AnoCar1,AnoCar2,AnoGam1,ApiMel1,ApiMel2,ApiMel3,ApiMel4,AplCal1,AscSuu1,BosTau1,BosTau2,BosTau3,BosTau4,BosTau6,BosTau7,BosTau8,BosTau9,BraFlo1,BraFlo2,BruMal1,BruMal2,BurXyl1,CaeAng1,CaeAng2,CaeJap1,CaeJap3,CaeJap4,CaePb1,CaePb2,CaePb3,CaeRem2,CaeRem3,CaeRem4,CaeSp111,CaeSp51,CalJac1,CalJac3,CalMil1,CanFam1,CanFam2,CanFam3,CanFamPoodle1,CavPor3,Cb1,Cb3,Cb4,Ce2,Ce4,Ce6,Ce9,Ce10,Ce11,ChlSab1,ChlSab2,ChoHof1,ChrPic2,Ci1,Ci2,CioSav2,ColAng1,CriGri1,CriGriChoV1,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,DanRer7,DanRer10,DasNov2,DasNov3,DipOrd1,DirImm1,Dm1,Dm2,Dm3,Dm6,Dp1,Dp2,Dp3,Dp4,DroAlb1,DroAna1,DroAna2,DroAna3,DroBia2,DroBip2,DroEle2,DroEre1,DroEre2,DroEug2,DroFic2,DroGri1,DroGri2,DroKik2,DroMir2,DroMoj1,DroMoj2,DroMoj3,DroPer1,DroPse3,DroRho2,DroSec1,DroSim1,DroSuz1,DroTak2,DroVir1,DroVir2,DroVir3,DroWil1,DroWil2,DroYak1,DroYak2,DroYak3,EchTel1,EquCab1,EquCab2,EquCab3,EriEur1,EriEur2,FalPer1,FelCat3,FelCat4,FelCat5,FelCat8,FelCat9,Fr1,Fr2,Fr3,GadMor1,GalGal2,GalGal3,GalGal4,GalGal5,GalGal6,GalVar1,GasAcu1,GeoFor1,GorGor1,GorGor2,GorGor3,GorGor4,GorGor5,HaeCon1,HaeCon2,HetBac1,HetGla1,HetGla2,Hg16,Hg17,Hg18,Hg19,Hg19Patch2,Hg19Patch5,Hg19Patch9,Hg19Patch10,Hg19Patch13,Hg38Patch2,Hg38Patch3,Hg38Patch5,Hg38Patch6,Hg38Patch7,Hg38Patch9,Hg38Patch11,Hg38,LatCha1,LepWed1,LoaLoa1,LoxAfr2,LoxAfr3,MacEug1,MacEug2,MacFas5,MarVir1,MayZeb1,MelGal1,MelGal5,MelHap1,MelInc1,MelInc2,MelUnd1,MesAur1,MicMur1,MicMur2,MicMur3,MicOch1,Mm5,Mm6,Mm7,Mm8,Mm9,Mm10,Mm10Patch1,Mm10Patch4,MonDom1,MonDom2,MonDom4,MonDom5,MusDom2,MyoLuc1,MyoLuc2,NanPar1,NasLar1,NecAme1,NomLeu1,NomLeu2,NomLeu3,OchPri2,OncVol1,OreNil1,OreNil2,OreNil3,OrnAna1,OrnAna2,OryCun1,OryCun2,OryLat1,OryLat2,OtoGar1,OtoGar3,OviAri1,OviAri3,OviAri4,PanPan1,PanRed1,PanTro1,PanTro2,PanTro3,PanTro4,PanTro5,PanTro6,PapAnu2,PapAnu3,PapHam1,PelSin1,PetMar1,PetMar2,PetMar3,PonAbe2,PonAbe3,PriExs1,PriPac1,PriPac2,PriPac3,ProCap1,ProCoq1,PteVam1,RheMac1,RheMac2,RheMac3,RheMac8,RheMac10,RhiRox1,Rn3,Rn4,Rn5,Rn6,RegenRn0,SaiBol1,SorAra1,SpeTri1,SpeTri2,StrRat1,StrRat2,StrPur1,StrPur2,SusScr1,SusScr2,SusScr3,SusScr11,TaeGut1,TaeGut2,TarSyr1,TarSyr2,TetNig1,TetNig2,TriCas2,TriMan1,TriSpi1,TriSui1,TupBel1,TurTle1,TurTru1,TurTru2,VicPac1,VicPac2,XenLae2,XenTro1,XenTro2,XenTro3,XenTro7,XenTro9
 
 # Define databases that support known genes
 set kgDb $hg,$mm,rn3
 # Older format (KG 2)
 set kgDb2 hg16,hg17,mm7,mm8,rn3,rn4
 # Newer format (KG 3 aka UCSC Genes)
 set kgDb3 hg18,hg19,hg38,mm9,mm10
 
 # Protein browser databases.
 set pbDb hg18,hg17,hg16,mm7,mm8,mm9,rn3
 set pbDb1 hg17,hg16,mm7,mm8,mm9,rn3
 set pbDb2 rn3
 set pbDb3 hg16,hg17,hg18
 
 # Define databases that support family browser (gene sorter)
@@ -4991,31 +4991,31 @@
     $hgSplit,hg19,!hg18.gl.frag $split chopAfter=_
     $hg,!hg16,!hg17,!hg18.gold.frag
     $hgSplit,!hg18.gold.frag $split
     hg18.gl.frag $split chopAfter=_ minCheck=0.95
     hg18.gold.frag $split minCheck=0.90
 
 identifier wgsContigAccession typeOf=seqExtFile
 "Genbank accession.version of whole-genome shotgun contig"
     $wgs.contigAcc.acc
 
 identifier wgsContigName
 "Sequencing project name for whole-genome shotgun contigs."
     $wgs.contigAcc.contig
     $wgs,!panTro1.gold.frag $split full
 
-set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rhiBie1,!rhiRox1,!rn5,!rn6,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier proteinAccession fuzzy
 "Genbank protein accession."
     $kgDb.kgProtAlias.alias
     $kgDb.kgSpAlias.alias minCheck=0.1
     $kgDb.kgXref.protAcc
     hgFixed.refLink.protAcc
 
 identifier estOrMrnaAccession
 "Genbank EST or mRNA accession."
     hgFixed.gbSeq.acc
     hgFixed.gbCdnaInfo.acc unique
     hgFixed.imageClone.acc
     $gbd,!ce2,!hg16,!hg17,!hg18,!mm7.altGraphX.mrnaRefs comma
     ce2.altGraphX.mrnaRefs comma minCheck=0.96
@@ -5570,52 +5570,52 @@
 "An image cDNA clone ID"
     hgFixed.imageClone.imageId
 
 identifier humanFosmidId
 "Human Fosmid (~50kb genomic sequence) clone"
     $hg.fosEndPairs.name dupeOk
 
 identifier humanFosmidEndId
 "Identifier of read from one end of human formid."
     $hg.all_fosends.qName dupeOk
     $hg.fosEndPairs.lfNames comma
 
 ## TYPED TO HERE %%%
 # Mapping Stuff, STS, etc.
 
-set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rhiBie1,!rhiRox1,!rn5,!rn6,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier dbStsId external=dbSts fuzzy
 "NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID"
     $hg.all_sts_primer.qName chopBefore=dbSTS_
     $gbd,$notDbStsId.all_sts_seq.qName
     $gbd,$notDbStsId.stsInfo2.dbSTSid
 
 identifier ucscStsId
 "UCSC STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $gbd.stsInfo2.identNo
     $gbd.stsAlias.identNo
     $gbd.stsMap.identNo
 
 identifier ucscMouseStsId
 "UCSC Mouse STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $mm.stsInfoMouseNew.identNo
     $mm.stsAlias.identNo
     $mm.all_sts_primer.qName chopAfter=_ minCheck=0.99
     $mm.stsMapMouseNew.identNo
 
-set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rhiBie1,!rhiRox1,!rn5,!rn6,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier stsName fuzzy
 "STS (Sequenced Tagged Site, aka mapping sequence) Name"
     $hg.fishClones.stsNames comma
     $gbd,$notStsName.stsInfo2.otherNames comma
     $mm.stsInfoMouseNew.alias separator=;
 
 identifier stsTrueName typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
     $gbd,!hg16.stsInfo2.name
     $gbd.stsAlias.trueName
     $gbd.stsMap.name
 
 identifier stsTrueNameHg16 typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name for hg16"
@@ -5700,31 +5700,31 @@
     $hg.jaxOrtholog.mouseSymbol
     hgFixed.refLink.name
     visiGene.gene.name
 
 # Model Organism Database Identifiers
 
 identifier jaxMgiId
 "Jackson Labs Mouse Gene Identifier"
     $hg.jaxOrtholog.mgiId
 
 identifier wormBaseIsoformCluster
 "Overlapping (after splicing) WormBase transcripts"
     $ce.sangerCanonical.clusterId
     $ce.sangerIsoforms.clusterId full
 
-set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenRn0,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier wormBaseId external=WormBase dependency
 "WormBase (C. elegans) ORF ID"
     $ce.sangerGene.name
     $gbd,$notWormBaseId.ceBlastTab.target minCheck=0.90
     $ce.kimExpDistance.query minCheck=0.68
     $ce.kimExpDistance.target minCheck=0.66
     $ce.orfToGene.name
     $ce.sangerBlastTab.query
     $ce.sangerBlastTab.target
     $ce.sangerCanonical.transcript
     $ce.sangerIsoforms.transcript
     $ce.sangerLinks.orfName minCheck=0.96
     $ce.sangerPep.name minCheck=0.96
     $ce.sangerToKim.name
@@ -5744,31 +5744,31 @@
 
 identifier wormBaseRnaGene external=WormBase dependency
 "WormBase (C. elegans) RNA genes"
     $ce.sangerRnaGene.name
 
 identifier flyBaseRefId
 "FlyBase (Drosophila) Reference (Literature)"
     $dm.fbRef.id
     $dm.fbPhenotype.fbRef
 
 identifier flyBaseAlleleId
 "FlyBase (Drosophila) Allele ID"
     $dm.fbAllele.id
     $dm.fbPhenotype.fbAllele exclude=0
 
-set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenRn0,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier flyBaseGeneId external=FlyBase
 "FlyBase (Drosophila) Gene ID"
     $dm.fbGene.geneId
     $dm.bdgpExprLink.flyBaseId minCheck=0.95
     dm1.bdgpGeneInfo.flyBaseId minCheck=0.95
     dm1.bdgpNonCodingInfo.flyBaseId minCheck=0.20
     dm1.bdgpSwissProt.flyBaseId minCheck=0.95
     $dm.fbAllele.geneId
     $dm.fbPhenotype.geneId
     $dm.fbSynonym.geneId
     $dm.fbTranscript.geneId minCheck=0.95
     dm1.flyBaseSwissProt.flyBaseId minCheck=0.95
     $dm,!dm1.flyBase2004Xref.fbgn minCheck=0.90
     $dm,!dm1.pscreen.geneIds comma minCheck=0.95
@@ -5862,31 +5862,31 @@
     $dm.flyreg2.name minCheck=0.8
 
 identifier sgdIsoformCluster
 "Overlapping (after splicing) SGD (Yeast) transcripts"
     $sacCer.sgdCanonical.clusterId
     $sacCer.sgdIsoforms.clusterId full
 
 identifier sgdProtHomologId
 "sacCer protHomolog protein ID"
     $sacCer.protHomolog.proteinID dupeOk
     $sacCer.samSubdir.proteinId
 
 identifier sgdId external=SGD
 "Sacchromyces Genome Database ID - Coding or other"
 
-set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rhiBie1,!rhiRox1,!rn5,!rn6,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier sgdCodingId typeOf=sgdId dependency
 "Sacchromyces Genome Database ID"
     $sacCer.sgdGene.name
     $gbd,$notSgdCodingId.scBlastTab.target minCheck=0.90
     $sacCer.sgdBlastTab.query
     $sacCer.sgdBlastTab.target
     $sacCer.ceBlastTab.query
     $sacCer.dmBlastTab.query
     $sacCer,!sacCer1.drBlastTab.query
     $sacCer.hgBlastTab.query minCheck=0.999
     $sacCer.mmBlastTab.query
     $sacCer.rnBlastTab.query
     sacCer2.knownBlastTab.query
     $sacCer.choExpDistance.target minCheck=0.60
@@ -6004,31 +6004,31 @@
 "Ensemble Gene ID"
     $gbd.ensemblXref3.gene dupeOk
 
 identifier ensemblProteinId external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensTranscript.translation_name dupeOk
     $gbd.ensGtp.protein chopAfter=.
     $gbd.sfAssign.seqID minCheck=0.01
 
 identifier ensemblProteinId3 external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensemblXref3.protein dupeOk
     $gbd.sfAssign.seqID minCheck=0.01
 
 
-set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!xenLae2,!xenTro7,!xenTro9
+set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenRn0,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!xenLae2,!xenTro7,!xenTro9
 
 identifier ensemblTranscriptId external=Ensembl dependency
 "Ensembl Transcript ID"
     $ensGeneDb,$notEnsemblTranscriptId.ensGene.name dupeOk
     $gbd,$notEnsemblTranscriptId.ensGeneXref.transcript_name minCheck=0.95
     $ensGeneDb,$notEnsemblTranscriptId.ensGtp.transcript minCheck=0.94
     $ensGeneDb,$notEnsemblTranscriptId.ensPep.name minCheck=0.93
     $gbd,$notEnsemblTranscriptId.ensTranscript.transcript_name minCheck=0.20
     $gbd,$notEnsemblTranscriptId.ensInfo.name minCheck=0.9
     $ensGeneDb,$notEnsemblTranscriptId.ensemblToGeneName.name minCheck=0.94
     $ensGeneDb,$notEnsemblTranscriptId.ensemblSource.name minCheck=0.96
     !hg38,$kgDb.knownToEnsembl.value chopAfter=.
     $kgDb.rgdGene2ToEnsembl.value chopAfter=.
     $danRer.ensZfishBlastTab.query
     $danRer.ensZfishBlastTab.target