11a82397d8d5c6d013cc62cdc99b84bc5506747e braney Fri Jul 17 12:55:23 2020 -0700 ongoing work on the GENCODE merge diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner index 2665775..370aad6 100644 --- src/hg/makeDb/schema/all.joiner +++ src/hg/makeDb/schema/all.joiner @@ -137,34 +137,35 @@ 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 set tupChi tupChi1 set turTru turTru1,turTru2 set vicPac vicPac1,vicPac2 set wuhCor wuhCor1 set xenLae xenLae2 set xenTro xenTro1,xenTro2,xenTro3,xenTro7,xenTro9 set xipMac xipMac1 +set braNey braNey38 # 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 +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 # 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 @@ -5400,106 +5401,52 @@ mm10.wgEncodeGencodeAnnotationRemarkVM25.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.10 identifier wgEncodeGencodeEntrezGeneVM25 "Link together Gencode UniProt Support table with Attributes table" mm10.wgEncodeGencodeEntrezGeneVM25.transcriptId dupeOk mm10.wgEncodeGencodeEntrezGeneVM25.transcriptId minCheck=0.35 identifier wgEncodeGencodeExonSupportVM25 "Link together Gencode Exon Support table with Attributes table" mm10.wgEncodeGencodeExonSupportVM25.transcriptId dupeOk mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.90 # end Gencode VM25 -# begin Gencode V35 (2020 reorganization) - -identifier gencodeAnnotAttrsV35 +identifier gencodeAnnotV35 "Link together Gencode Annotation Table with Attributes table" - hg38.gencodeAttrsV35.transcriptId - hg38.gencodeAnnotV35.name - -# gencode association tables (joined through gencodeAttrsV35) -identifier gencodeGeneSourceV35 -"Link together Gencode Gene Source table with Attributes table" - hg38.gencodeGeneSourceV35.geneId - hg38.gencodeAttrsV35.geneId - -identifier gencodeGeneSymbolV35 -"Link together Gencode gene symbol table with Attributes table" - hg38.gencodeGeneSymbolV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.20 - -identifier gencodePdbV35 -"Link together Gencode Pdb table with Attributes table" - hg38.gencodePdbV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.015 - -identifier gencodePubMedV35 -"Link together Gencode Pubmed table with Attributes table" - hg38.gencodePubMedV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.63 - -identifier gencodeRefSeqV35 -"Link together Gencode RefSeq table with Attributes table" - hg38.gencodeRefSeqV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.05 - -identifier gencodeTagV35 -"Link together Gencode Tag table with Attributes table" - hg38.gencodeTagV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.36 - hg38.gencodeRefSeqV35.transcriptId minCheck=0.9 - -identifier gencodeTranscriptSourceV35 -"Link together Gencode Transcript Source table with Attributes table" - hg38.gencodeTranscriptSourceV35.transcriptId - hg38.gencodeAttrsV35.transcriptId - -identifier gencodeTranscriptSupportV35 -"Link together Gencode Transcript Support table with Attributes table" - hg38.gencodeTranscriptSupportV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.20 - -identifier gencodeTranscriptionSupportLevelV35 -"Link together Gencode Transcription Support Level table with Attributes table" - hg38.gencodeTranscriptionSupportLevelV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.30 - -identifier gencodeUniProtV35 -"Link together Gencode UniProt Support table with Attributes table" - hg38.gencodeUniProtV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.35 - -identifier gencodeAnnotationRemarkV35 -"Link together Gencode Annotation Remark table with Attributes table" - hg38.gencodeAnnotationRemarkV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.10 - -identifier gencodeEntrezGeneV35 -"Link together Gencode UniProt Support table with Attributes table" - hg38.gencodeEntrezGeneV35.transcriptId dupeOk - hg38.gencodeEntrezGeneV35.transcriptId minCheck=0.35 - -identifier gencodeExonSupportV35 -"Link together Gencode Exon Support table with Attributes table" - hg38.gencodeExonSupportV35.transcriptId dupeOk - hg38.gencodeAttrsV35.transcriptId minCheck=0.80 - -# end Gencode V35 (2020 reorganization) - + $gbd.gencodeAttrsV35.transcriptId + $gbd.gencodeGeneSymbolV35.transcriptId + $gbd.gencodePdbV35.transcriptId + $gbd.gencodePubMedV35.transcriptId + $gbd.gencodeRefSeqV35.transcriptId + $gbd.gencodeTagV35.transcriptId + $gbd.gencodeRefSeqV35.transcriptId minCheck=0.9 + $gbd.gencodeTranscriptSourceV35.transcriptId minCheck=0.9 + $gbd.gencodeTranscriptSupportV35.transcriptId + $gbd.gencodeTranscriptionSupportLevelV35.transcriptId + $gbd.gencodeUniProtV35.transcriptId + $gbd.gencodeAnnotationRemarkV35.transcriptId minCheck=0.9 + $gbd.gencodeEntrezGeneV35.transcriptId + $gbd.gencodeExonSupportV35.transcriptId + $gbd.gencodeAnnotV35.name + +identifier gencodeAnnotV35Gene +"Link together Gencode Annotation Table with Attributes table" + $gbd.gencodeGeneSourceV35.geneId + $gbd.gencodeAttrsV35.geneId identifier wgEncodeGencodeClassesV3Hg19 "Link together Gencode gene model (Known) and class for July 2009 Data Version" hg19.wgEncodeGencodeClassesV3.name hg19.wgEncodeGencodeAutoV3.name unique hg19.wgEncodeGencodeManualV3.name unique hg19.wgEncodeGencodePolyaV3.name unique identifier acemblyName dependency "Link together Acembly gene model structure and peptide." $hg,$mm.acembly.name $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90 hg17.acemblyPep.name unique minCheck=0.63 $hg,$mm.acemblyClass.name full unique