ac3f2a02f179d651cdcb328ac93f77d18ef2459c braney Fri Aug 9 16:06:29 2019 -0700 move unused type blocks to end of file and add pithy comment about them only being used by joinerGraph refs #5396 diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index 254fd5e..c794009 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -7399,246 +7399,30 @@ dependency $pbDb.pbAaDistI $pbDb.knownGenePep dependency $pbDb.pbAaDistK $pbDb.knownGenePep dependency $pbDb.pbAaDistL $pbDb.knownGenePep dependency $pbDb.pbAaDistM $pbDb.knownGenePep dependency $pbDb.pbAaDistN $pbDb.knownGenePep dependency $pbDb.pbAaDistP $pbDb.knownGenePep dependency $pbDb.pbAaDistQ $pbDb.knownGenePep dependency $pbDb.pbAaDistR $pbDb.knownGenePep dependency $pbDb.pbAaDistS $pbDb.knownGenePep dependency $pbDb.pbAaDistT $pbDb.knownGenePep dependency $pbDb.pbAaDistV $pbDb.knownGenePep dependency $pbDb.pbAaDistW $pbDb.knownGenePep dependency $pbDb.pbAaDistY $pbDb.knownGenePep -# Table types - only needed when the table does not have the same name .as file record. -type genePred - $hg.acembly - $gbd.ECgene - $gbd.geneid - $gbd.genscan - $gbd.sgpGene - $gbd.softberryGene - $gbd.twinscan - $gbd.ensGene - $gbd.vegaGene - $gbd.refGene - $gbd.xenoRefGene - $gbd.jgiFilteredModels - $gbd.geneMapper - -type pepPred - $hg.acemblyPep - $gbd.ECgenePep - $gbd.geneidPep - $gbd.genscanPep - $gbd.sgpPep - $gbd.softberryPep - $gbd.twinscanPep - $gbd.ensPep - $gbd.vegaPep - $gbd.knownGenePep - $ce.sangerPep - dm1.bdgpGenePep - $dm.flyBasePep - -type psl - $hg.affyU95 - $hg.affyU133 - $hg.affyU133Plus2 - $hg.HInvGeneMrna - $mm.affyU74 - $danRer.affyZebrafish - $gbd.all_bacends - $gbd.all_fosends - $gbd.all_est - $gbd.est - $gbd.intronEst - $gbd.xenoEst - $gbd.xenoMrna - $gbd.all_mrna - $gbd.refSeqAli - $gbd.all_sts_primer - $gbd.all_sts_seq - -type estOrientInfo - $gbd.estOrientInfo - $gbd.mrnaOrientInfo - -type expRecord - hgFixed.nci60Exps - hgFixed.rosettaExps - hgFixed.affyExps.id - hgFixed.gnfHumanU95AllExps - hgFixed.gnfHumanU95MedianExps - hgFixed.gnfMouseU74aAllExps - hgFixed.gnfMouseU74aMedianExps - hgFixed.gnfMouseU74bAllExps - hgFixed.gnfMouseU74bMedianExps - hgFixed.gnfMouseU74cAllExps - hgFixed.gnfMouseU74cMedianExps - hgFixed.arbFlyLifeAllExps - hgFixed.arbFlyLifeMedianExps - hgFixed.kimWormLifeAllExps - hgFixed.kimWormLifeMedianExps - hgFixed.yeastChoCellCycleExps - hgFixed.gladHumESExps - -type expData - hgFixed.kimWormLifeAllRatio - hgFixed.kimWormLifeMedianRatio - hgFixed.gnfHumanU95All - hgFixed.gnfHumanU95AllRatio - hgFixed.gnfHumanU95Median - hgFixed.gnfHumanU95MedianRatio - hgFixed.gnfMouseU74aAll - hgFixed.gnfMouseU74aAllRatio - hgFixed.gnfMouseU74aMedian - hgFixed.gnfMouseU74aMedianRatio - hgFixed.gnfMouseU74bAll - hgFixed.gnfMouseU74bAllRatio - hgFixed.gnfMouseU74bMedian - hgFixed.gnfMouseU74bMedianRatio - hgFixed.gnfMouseU74cAll - hgFixed.gnfMouseU74cAllRatio - hgFixed.gnfMouseU74cMedian - hgFixed.gnfMouseU74cMedianRatio - hgFixed.arbFlyLifeAll - hgFixed.arbFlyLifeAllRatio - hgFixed.arbFlyLifeMedian - hgFixed.arbFlyLifeMedianRatio - hgFixed.kimWormLifeAllRatio - hgFixed.kimWormLifeMedianRatio - hgFixed.yeastChoCellCycle - hgFixed.yeastChoCellCycleRatio - hgFixed.gladHumES - hgFixed.gladHumESRatio - -type exprBed - $hg.affyRatio - $mm.affyGnfU74A - $mm.affyGnfU74B - $mm.affyGnfU74C - $hg.nci60 - $rn.gnfAtlas2 - # hgFixed.rosChr22Dat - -type expDistance - $hg.gnfAtlas2Distance - $hg.gnfU95Distance - $mm.affyGnfU74ADistance - $mm.affyGnfU74BDistance - $mm.affyGnfU74CDistance - $mm.mouseLandscapeDistance - $hg.knownGnfDistance - $ce.kimExpDistance - $dm.arbExpDistance - $sacCer.choExpDistance - $hg.gladHumESDistance - -type chain - $gbd.chr%_chain% - $gbd.chr%_chainSelf - -type agpFrag - $gbd.chr%_gold - -type agpGap - $gbd.chr%_gap - -type gl - $gbd.chr%_gl - -type knownTo - $gbd.knownToCdsSnp - $gbd.knownToEnsembl - $gbd.knownToLocusLink - $gbd.knownToPfam - $gbd.knownToRefSeq - $gbd.knownToAllenBrain - $hg.knownToU95 - $hg.knownToU133 - $hg.knownToU133Plus2 - $hg.knownToHInv - $mm.knownToU74 - $mm.knownToXM - $ce.sangerToKim - $ce.sangerToPfam - $ce.sangerToRefSeq - dm1.bdgpToLocusLink - dm1.bdgpToPfam - dm1.bdgpToRefSeq - $sacCer.sgdToSwissProt - $sacCer.sgdToSgd - $sacCer.sgdToName - -type idName - hgFixed.source - hgFixed.organism - hgFixed.library - hgFixed.mrnaClone - hgFixed.sex - hgFixed.tissue - hgFixed.development - hgFixed.cell - hgFixed.cds - hgFixed.description - hgFixed.author - hgFixed.geneName - hgFixed.productName - hgFixed.keyword - -type blastTab - $gbd.ceBlastTab - $gbd.hgBlastTab - $gbd.dmBlastTab - $gbd.drBlastTab - $gbd.mmBlastTab - $gbd.rnBlastTab - $gbd.scBlastTab - $gbd.knownBlastTab - $ce.sangerBlastTab - dm1.bdgpBlastTab - sacCer1.sgdBlastTab - sacCer2.knownBlastTab - -type knownCanonical - $gbd.knownCanonical - $ce.sangerCanonical - dm1.bdgpCanonical - $sacCer.sgdCanonical - -type knownIsoforms - $gbd.knownIsoforms - $ce.sangerIsoforms - dm1.bdgpIsoforms - $sacCer.sgdIsoforms - -type rnaFold - $gbd.foldUtr3 - $gbd.foldUtr5 - -type bed - $gbd.vegaPseudoGene - $sacCer.sgdOther - -type geneAndProt - $kgDb.knownGene - $ce.sangerGene - dm1.bdgpGene - $sacCer.sgdGene # Ignored tables - no linkage here that we check at least. tablesIgnored go instance_data source_audit tablesIgnored visiGene vgPrbAli vgPrbAliAll tableDescriptions tablesIgnored hgFixed omimTitle cutters @@ -8514,15 +8298,235 @@ tablesIgnored $xenLae tableList tablesIgnored $xenTro tableList tablesIgnored hg18 phastBiasTracts3 phastBiasPosteriors3 phastBiasChimpTracts3 phastBiasChimpPosteriors3 tablesIgnored $tRNAsDbs tRNAs + +# Table types - only used in joinerGraph which is not part of the standard build and probably +# doesn't work anymore. Probably not worth updating, but someone may want to resurrect +# joinerGraph so here they are. +type genePred + $hg.acembly + $gbd.ECgene + $gbd.geneid + $gbd.genscan + $gbd.sgpGene + $gbd.softberryGene + $gbd.twinscan + $gbd.ensGene + $gbd.vegaGene + $gbd.refGene + $gbd.xenoRefGene + $gbd.jgiFilteredModels + $gbd.geneMapper + +type pepPred + $hg.acemblyPep + $gbd.ECgenePep + $gbd.geneidPep + $gbd.genscanPep + $gbd.sgpPep + $gbd.softberryPep + $gbd.twinscanPep + $gbd.ensPep + $gbd.vegaPep + $gbd.knownGenePep + $ce.sangerPep + dm1.bdgpGenePep + $dm.flyBasePep + +type psl + $hg.affyU95 + $hg.affyU133 + $hg.affyU133Plus2 + $hg.HInvGeneMrna + $mm.affyU74 + $danRer.affyZebrafish + $gbd.all_bacends + $gbd.all_fosends + $gbd.all_est + $gbd.est + $gbd.intronEst + $gbd.xenoEst + $gbd.xenoMrna + $gbd.all_mrna + $gbd.refSeqAli + $gbd.all_sts_primer + $gbd.all_sts_seq + +type estOrientInfo + $gbd.estOrientInfo + $gbd.mrnaOrientInfo + +type expRecord + hgFixed.nci60Exps + hgFixed.rosettaExps + hgFixed.affyExps.id + hgFixed.gnfHumanU95AllExps + hgFixed.gnfHumanU95MedianExps + hgFixed.gnfMouseU74aAllExps + hgFixed.gnfMouseU74aMedianExps + hgFixed.gnfMouseU74bAllExps + hgFixed.gnfMouseU74bMedianExps + hgFixed.gnfMouseU74cAllExps + hgFixed.gnfMouseU74cMedianExps + hgFixed.arbFlyLifeAllExps + hgFixed.arbFlyLifeMedianExps + hgFixed.kimWormLifeAllExps + hgFixed.kimWormLifeMedianExps + hgFixed.yeastChoCellCycleExps + hgFixed.gladHumESExps + +type expData + hgFixed.kimWormLifeAllRatio + hgFixed.kimWormLifeMedianRatio + hgFixed.gnfHumanU95All + hgFixed.gnfHumanU95AllRatio + hgFixed.gnfHumanU95Median + hgFixed.gnfHumanU95MedianRatio + hgFixed.gnfMouseU74aAll + hgFixed.gnfMouseU74aAllRatio + hgFixed.gnfMouseU74aMedian + hgFixed.gnfMouseU74aMedianRatio + hgFixed.gnfMouseU74bAll + hgFixed.gnfMouseU74bAllRatio + hgFixed.gnfMouseU74bMedian + hgFixed.gnfMouseU74bMedianRatio + hgFixed.gnfMouseU74cAll + hgFixed.gnfMouseU74cAllRatio + hgFixed.gnfMouseU74cMedian + hgFixed.gnfMouseU74cMedianRatio + hgFixed.arbFlyLifeAll + hgFixed.arbFlyLifeAllRatio + hgFixed.arbFlyLifeMedian + hgFixed.arbFlyLifeMedianRatio + hgFixed.kimWormLifeAllRatio + hgFixed.kimWormLifeMedianRatio + hgFixed.yeastChoCellCycle + hgFixed.yeastChoCellCycleRatio + hgFixed.gladHumES + hgFixed.gladHumESRatio + +type exprBed + $hg.affyRatio + $mm.affyGnfU74A + $mm.affyGnfU74B + $mm.affyGnfU74C + $hg.nci60 + $rn.gnfAtlas2 + # hgFixed.rosChr22Dat + +type expDistance + $hg.gnfAtlas2Distance + $hg.gnfU95Distance + $mm.affyGnfU74ADistance + $mm.affyGnfU74BDistance + $mm.affyGnfU74CDistance + $mm.mouseLandscapeDistance + $hg.knownGnfDistance + $ce.kimExpDistance + $dm.arbExpDistance + $sacCer.choExpDistance + $hg.gladHumESDistance + +type chain + $gbd.chr%_chain% + $gbd.chr%_chainSelf + +type agpFrag + $gbd.chr%_gold + +type agpGap + $gbd.chr%_gap + +type gl + $gbd.chr%_gl + +type knownTo + $gbd.knownToCdsSnp + $gbd.knownToEnsembl + $gbd.knownToLocusLink + $gbd.knownToPfam + $gbd.knownToRefSeq + $gbd.knownToAllenBrain + $hg.knownToU95 + $hg.knownToU133 + $hg.knownToU133Plus2 + $hg.knownToHInv + $mm.knownToU74 + $mm.knownToXM + $ce.sangerToKim + $ce.sangerToPfam + $ce.sangerToRefSeq + dm1.bdgpToLocusLink + dm1.bdgpToPfam + dm1.bdgpToRefSeq + $sacCer.sgdToSwissProt + $sacCer.sgdToSgd + $sacCer.sgdToName + +type idName + hgFixed.source + hgFixed.organism + hgFixed.library + hgFixed.mrnaClone + hgFixed.sex + hgFixed.tissue + hgFixed.development + hgFixed.cell + hgFixed.cds + hgFixed.description + hgFixed.author + hgFixed.geneName + hgFixed.productName + hgFixed.keyword + +type blastTab + $gbd.ceBlastTab + $gbd.hgBlastTab + $gbd.dmBlastTab + $gbd.drBlastTab + $gbd.mmBlastTab + $gbd.rnBlastTab + $gbd.scBlastTab + $gbd.knownBlastTab + $ce.sangerBlastTab + dm1.bdgpBlastTab + sacCer1.sgdBlastTab + sacCer2.knownBlastTab + +type knownCanonical + $gbd.knownCanonical + $ce.sangerCanonical + dm1.bdgpCanonical + $sacCer.sgdCanonical + +type knownIsoforms + $gbd.knownIsoforms + $ce.sangerIsoforms + dm1.bdgpIsoforms + $sacCer.sgdIsoforms + +type rnaFold + $gbd.foldUtr3 + $gbd.foldUtr5 + +type bed + $gbd.vegaPseudoGene + $sacCer.sgdOther + +type geneAndProt + $kgDb.knownGene + $ce.sangerGene + dm1.bdgpGene + $sacCer.sgdGene + }