411acf92db70f5f7a8584cb3cad643b88d4aeabc
hiram
  Mon Sep 14 15:04:51 2020 -0700
additional rules for canFam5 refs #25917

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index f598ba6..c8fd089 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -153,31 +153,31 @@
 
 
 # Define all organism/assembly-specific databases.
 set gbd $ailMel,$allMis,$ambMex,$anaPla,$anoCar,$anoGam,$aotNan,$apiMel,$aplCal,$aptMan,$aquChr,$astMex,$balAcu,$bisBis,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$canFam,$calJac,$calMil,$casCan,$cavApe,$cavPor,$cb,$ce,$cebCap,$cerAty,$cerSim,$chiLan,$choHof,$chlSab,$chrPic,$ci,$cioSav,$colAng,$cotJap,$criGri,$danRer,$dasNov,$dipOrd,$dm,$dp,$droMult,$droYak,$eboVir,$echTel,$enhLutNer,$equCab,$eriEur,$eulFla,$eulMac,$felCat,$ficAlb,$fr,$fukDam,$gadMor,$galGal,$gasAcu,$galVar,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$jacJac,$latCha,$lepOcu,$loxAfr,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$melUnd,$mesAur,$micMur,$micOch,$mm,$monDom,$musFur,$myoLuc,$nanGal,$nanPar,$nasLar,$neoSch,$nomLeu,$ochPri,$octDeg,$orcOrc,$oreNil,$ornAna,$oryCun,$oryLat,$otoGar,$oviAri,$oxyTri,$panPan,$panManBai,$panTro,$papAnu,$papHam,$pelSin,$petMar,$perMan,$poeFor,$ponAbe,$priPac,$proCap,$proCoq,$pteVam,$rheMac,$rhiBie,$rhiRox,$rn,$rouAeg,$sacCer,$saiBol,$sarHar,$sorAra,$speTri,$staAur,$strPur,$susScr,$taeGut,$tarSyr,$tetNig,$thaSir,$triMan,$tupBel,$tupChi,$turTru,$vicPac,$wuhCor,$xenLae,$xenTro,$xipMac,$braNey
 
 set metaGbd $gbd
 
 # Define organism databases based on whole-genome shotgun projects
 # (Assembly based on WGS project contigs accessioned in Genbank)
 set wgs $ailMel,$allMis,$aplCal,$balAcu,$bisBis,$bosTau,$bruMal,$calJac,$calMil,$canFam,$cavPor,$choHof,$chrPic,$cioSav,$colAng,$cotJap,$criGri,$dasNov,$dipOrd,$echTel,$enhLutNer,$eriEur,$eulFla,$eulMac,$felCat,$fr,$galGal,$haeCon,$hetGla,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$micMur,$monDom,$musFur,$myoLuc,$nanPar,$nasLar,$neoSch,$nomLeu,$ochPri,$otoGar,$oryCun,$oryLat,$oviAri,$panPan,$panTro,$proCap,$proCoq,$pteVam,$rn,$sarHar,$sorAra,$speTri,$susScr,$taeGut,$tarSyr,$tetNig,$tupBel,$tupChi,$turTru,$vicPac
 
 # Define organism databases for which we build a xenoRefGene track:
 set xrg $ailMel,$allMis,$anoCar,$anoGam,$aotNan,$aplCal,$aquChr,$balAcu,$bisBis,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$calJac,$calMil,$canFam,$casCan,$cavApe,$cb,$ce,$cebCap,$cerAty,$cerSim,$chlSab,$choHof,$chrPic,$ci,$colAng,$cotJap,$criGri,danRer6,danRer7,danRer10,danRer11,$dasNov,$dipOrd,dm6,$dp,$droMult,$droYak,$echTel,$enhLutNer,$eriEur,$equCab,$eulFla,$eulMac,$felCat,$ficAlb,$fukDam,$gadMor,$galGal,$galVar,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$latCha,$loxAfr,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$melUnd,$mesAur,$micMur,$micOch,$mm,$monDom,$musFur,$myoLuc,$nanPar,$nasLar,$neoSch,$nomLeu,$ornAna,$ochPri,$orcOrc,$oreNil,$oryCun,$oryLat,$otoGar,$oviAri,$panPan,$panTro,$papAnu,$papHam,$petMar,$ponAbe,$priPac,$proCap,$proCoq,$pteVam,$rheMac,$rhiBie,$rhiRox,$rn,$rouAeg,$saiBol,$sarHar,$sorAra,$speTri,$staAur,$strPur,$susScr,$taeGut,$tarSyr,$thaSir,$triMan,$tupBel,$tupChi,$turTru,$vicPac,$xenLae,$xenTro
 
 # Ensembl gene track lists constructed from update procedure
-set ensGeneDb ailMel1,anaPla1,anoCar2,anoGam3,astMex1,bosTau6,calJac3,canFam2,canFam3,cavApe1,cavPor3,ce10,ce11,chiLan1,chlSab2,choHof1,ci2,ci3,cioSav2,criGri1,criGriChoV1,criGriChoV2,danRer10,danRer11,danRer7,dasNov2,dasNov3,dipOrd1,dipOrd2,dm3,dm6,echTel1,echTel2,equCab2,eriEur1,eriEur2,felCat3,felCat5,ficAlb1,fr2,fr3,fukDam1,gadMor1,galGal3,galGal4,galGal5,gasAcu1,gorGor3,gorGor4,hetGla1,hetGla2,hg16,hg17,hg18,hg19,hg38,jacJac1,latCha1,lepOcu1,loxAfr3,macEug1,melGal1,mesAur1,micMur1,micMur2,micOch1,mm10,mm7,mm8,mm9,monDom5,musFur1,myoLuc2,nanGal1,nomLeu1,nomLeu3,ochPri2,ochPri3,octDeg1,oreNil1,ornAna1,ornAna2,oryCun2,oryLat2,otoGar3,oviAri3,panTro2,panTro4,papAnu2,papAnu3,papAnu4,pelSin1,perManBai1,petMar2,poeFor1,ponAbe2,proCap1,pteVam1,regenCho1,rheMac2,rheMac8,rn3,rn4,rn5,rn6,sacCer3,saiBol1,sarHar1,sorAra1,sorAra2,speTri2,susScr1,susScr11,susScr3,taeGut1,tarSyr1,tetNig2,tupBel1,turTru1,vicPac1,vicPac2,xenTro3,xipMac1
+set ensGeneDb ailMel1,anaPla1,anoCar2,anoGam3,astMex1,bosTau6,calJac3,canFam2,canFam3,canFam5,cavApe1,cavPor3,ce10,ce11,chiLan1,chlSab2,choHof1,ci2,ci3,cioSav2,criGri1,criGriChoV1,criGriChoV2,danRer10,danRer11,danRer7,dasNov2,dasNov3,dipOrd1,dipOrd2,dm3,dm6,echTel1,echTel2,equCab2,eriEur1,eriEur2,felCat3,felCat5,ficAlb1,fr2,fr3,fukDam1,gadMor1,galGal3,galGal4,galGal5,gasAcu1,gorGor3,gorGor4,hetGla1,hetGla2,hg16,hg17,hg18,hg19,hg38,jacJac1,latCha1,lepOcu1,loxAfr3,macEug1,melGal1,mesAur1,micMur1,micMur2,micOch1,mm10,mm7,mm8,mm9,monDom5,musFur1,myoLuc2,nanGal1,nomLeu1,nomLeu3,ochPri2,ochPri3,octDeg1,oreNil1,ornAna1,ornAna2,oryCun2,oryLat2,otoGar3,oviAri3,panTro2,panTro4,papAnu2,papAnu3,papAnu4,pelSin1,perManBai1,petMar2,poeFor1,ponAbe2,proCap1,pteVam1,regenCho1,rheMac2,rheMac8,rn3,rn4,rn5,rn6,sacCer3,saiBol1,sarHar1,sorAra1,sorAra2,speTri2,susScr1,susScr11,susScr3,taeGut1,tarSyr1,tetNig2,tupBel1,turTru1,vicPac1,vicPac2,xenTro3,xipMac1
 
 # Databases from the old days when we split some large tables into one table per chrom
 # Some databases are excluded here because they're excluded from databasesChecked, e.g. cb2, ce3
 set oldSplit anoGam1,apiMel2,bosTau3,bosTau4,braFlo1,caeJap1,caePb1,caePb2,caeRem2,caeRem3,canFam1,canFam2,cb1,cb3,cb4,ce10,ce2,ce4,ce6,ce9,danRer3,danRer4,dm1,dm2,dm3,dp3,droSim1,droYak1,droYak2,equCab1,equCab2,fr1,fr2,galGal2,galGal3,gasAcu1,hg16,hg17,hg18,mm10,mm7,mm8,mm9,monDom1,monDom4,panTro1,panTro2,ponAbe2,priPac1,rheMac2,rn3,rn4,sacCer1,sacCer2,sacCer3,strPur2,susScr1,susScr2,taeGut1,tetNig1,tetNig2
 
 set hgSplit hg16,hg17,hg18
 
 # Obsolete archived Ensembl gene tracks
 set obsoleteEnsGeneDb danRer7,hg16,hg38,rn3
 
 set ensGeneWgs chlSab2,choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,eriEur2,felCat3,gadMor1,micMur1,myoLuc2,ochPri2,ochPri3,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1,vicPac2
 
 set ensGeneScaffold choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,eriEur2,felCat3,gadMor1,micMur1,ochPri2,ochPri3,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1,vicPac2
 
 # Define organism databases for which we host the vegaGenes
@@ -7070,31 +7070,31 @@
 "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,!calJac4,!canFam4,!canFam5,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!mm39,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!calJac4,!canFam4,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!mm39,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!wuhCor1,!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,!mm39.knownToEnsembl.value chopAfter=.
     $kgDb,!mm39.rgdGene2ToEnsembl.value chopAfter=.
     $danRer.ensZfishBlastTab.query
     $danRer.ensZfishBlastTab.target