bac632e3041cdfd281733475e9429cb283266e6c hiram Fri Mar 20 08:19:19 2020 -0700 adding tablesIgnored for wuhCor1 refs #25187 diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index 20f7939..6a4d77f 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -6143,52 +6143,52 @@ "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 $hg.fosEndPairs.lfNames comma ## TYPED TO HERE %%% # Mapping Stuff, STS, etc. -set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!regenCho1,!regenRn0,!regenRn1,!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,!gorGor6,!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,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!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 $mm.stsMapMouseNew.identNo -set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!regenCho1,!regenRn0,!regenRn1,!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,!gorGor6,!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,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!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" @@ -6274,31 +6274,31 @@ $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 $ce.sangerIsoforms.clusterId full -set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!regenCho1,!regenRn0,!regenRn1,!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,!gorGor6,!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,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!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 @@ -6318,31 +6318,31 @@ 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 $dm.fbPhenotype.fbAllele exclude=0 -set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!regenCho1,!regenRn0,!regenRn1,!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,!gorGor6,!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,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!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 @@ -6436,31 +6436,31 @@ $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 $sacCer.samSubdir.proteinId identifier sgdId external=SGD "Sacchromyces Genome Database ID - Coding or other" -set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!regenCho1,!regenRn0,!regenRn1,!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,!gorGor6,!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,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!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 @@ -6578,31 +6578,31 @@ "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,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!xenLae2,!xenTro7,!xenTro9 +set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!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.knownToEnsembl.value chopAfter=. $kgDb.rgdGene2ToEnsembl.value chopAfter=. $danRer.ensZfishBlastTab.query $danRer.ensZfishBlastTab.target @@ -8864,30 +8864,39 @@ tablesIgnored tarSyr2 tableList tablesIgnored tupBel1 tableList tablesIgnored tupChi1 tableList tablesIgnored vicPac1 tableList tablesIgnored vicPac2 tableList +tablesIgnored $wuhCor + genbank + mafSnp119way + mafSnp44way + mafSnpStrainName44way + primers + singleCover + singleCover44way + tablesIgnored $xenLae tableList tablesIgnored $xenTro tableList tablesIgnored hg18 phastBiasTracts3 phastBiasPosteriors3 phastBiasChimpTracts3 phastBiasChimpPosteriors3 tablesIgnored $tRNAsDbs tRNAs