733bfccc6366eca9cdb40718caff16406b38efee
hiram
  Wed Jun 26 14:41:14 2024 -0700
creating file to load into genomePriority.hgcentral for search purpose refs #32897

diff --git src/hg/hubApi/dbDb.name.clade.tsv src/hg/hubApi/dbDb.name.clade.tsv
new file mode 100644
index 0000000..ff45311
--- /dev/null
+++ src/hg/hubApi/dbDb.name.clade.tsv
@@ -0,0 +1,239 @@
+# manually curated list of dbDb assemblies to relate to GenArk clades
+# initial construction was via:
+#
+# grep -v "^#" UCSC* | cut -f3,6 | sort -u > genArk.sciName.clade.tsv
+# 
+# hgsql -hgenome-centdb -N -e \
+#  'select scientificName,name from dbDb where active=1;' hgcentral \
+#     | sort -u > dbDb.sciName.name.tsv
+# 
+# join -t $'\t' <(sort genArk.sciName.clade.tsv) \
+#    <(sort dbDb.sciName.name.tsv) | grep -v "(L)" \
+#    | awk -F$'\t' '{printf "%s\t%s\n", $3, $2}' | sort -u > dbDb.name.clade.tsv
+# 
+# sort -t$'\t' -k2,2 dbDb.sciName.name.tsv \
+#    | join -t $'\t' -1 2 -v1 - dbDb.name.clade.tsv > dbDb.name.missingClade.tsv
+#
+# then those few missingClade that didn't match were manually added
+# if new genomes are added to dbDb, they would need to be added here
+
+ailMel1	mammals
+allMis1	vertebrate
+anoCar1	vertebrate
+anoCar2	vertebrate
+anoGam1	invertebrate
+anoGam3	invertebrate
+apiMel1	invertebrate
+apiMel2	invertebrate
+aplCal1	invertebrate
+aptMan1	birds
+aquChr2	birds
+balAcu1	mammals
+bisBis1	mammals
+bosTau2	mammals
+bosTau3	mammals
+bosTau4	mammals
+bosTau6	mammals
+bosTau7	mammals
+bosTau8	mammals
+bosTau9	mammals
+braFlo1	invertebrate
+caeJap1	invertebrate
+caePb1	invertebrate
+caePb2	invertebrate
+caeRem2	invertebrate
+caeRem3	invertebrate
+calJac1	primates
+calJac3	primates
+calJac4	primates
+calMil1	vertebrate
+canFam1	mammals
+canFam2	mammals
+canFam3	mammals
+canFam4	mammals
+canFam5	mammals
+canFam6	mammals
+cavPor3	mammals
+cb1	invertebrate
+cb3	invertebrate
+ce10	invertebrate
+ce11	invertebrate
+ce2	invertebrate
+ce4	invertebrate
+ce6	invertebrate
+cerSim1	mammals
+chlSab2	primates
+choHof1	mammals
+chrPic1	vertebrate
+ci1	invertebrate
+ci2	invertebrate
+ci3	invertebrate
+criGri1	mammals
+criGriChoV1	mammals
+criGriChoV2	mammals
+danRer10	fish
+danRer11	fish
+danRer3	fish
+danRer4	fish
+danRer5	fish
+danRer6	fish
+danRer7	fish
+dasNov3	mammals
+dipOrd1	mammals
+dm1	invertebrate
+dm2	invertebrate
+dm3	invertebrate
+dm6	invertebrate
+dp2	invertebrate
+dp3	invertebrate
+droAna1	invertebrate
+droAna2	invertebrate
+droEre1	invertebrate
+droGri1	invertebrate
+droMoj1	invertebrate
+droMoj2	invertebrate
+droPer1	invertebrate
+droSec1	invertebrate
+droSim1	invertebrate
+droVir1	invertebrate
+droVir2	invertebrate
+droYak1	invertebrate
+droYak2	invertebrate
+eboVir3	viral
+echTel1	mammals
+echTel2	mammals
+enhLutNer1	mammals
+equCab1	mammals
+equCab2	mammals
+equCab3	mammals
+eriEur1	mammals
+eriEur2	mammals
+felCat3	mammals
+felCat4	mammals
+felCat5	mammals
+felCat8	mammals
+felCat9	mammals
+fr1	fish
+fr2	fish
+fr3	fish
+gadMor1	fish
+galGal2	birds
+galGal3	birds
+galGal4	birds
+galGal5	birds
+galGal6	birds
+galVar1	mammals
+gasAcu1	fish
+geoFor1	birds
+gorGor3	primates
+gorGor4	primates
+gorGor5	primates
+gorGor6	primates
+hetGla1	mammals
+hetGla2	mammals
+hg16	primates
+hg17	primates
+hg18	primates
+hg19	primates
+hg38	primates
+hs1	primates
+latCha1	vertebrate
+loxAfr3	mammals
+macEug2	mammals
+macFas5	primates
+manPen1	mammals
+melGal1	birds
+melGal5	birds
+melUnd1	birds
+micMur1	primates
+micMur2	primates
+mm10	mammals
+mm39	mammals
+mm7	mammals
+mm8	mammals
+mm9	mammals
+monDom1	mammals
+monDom4	mammals
+monDom5	mammals
+mpxvRivers	viral
+musFur1	mammals
+nanPar1	vertebrate
+nasLar1	primates
+neoSch1	mammals
+nomLeu1	primates
+nomLeu2	primates
+nomLeu3	primates
+ochPri2	mammals
+ochPri3	mammals
+oreNil2	fish
+ornAna1	mammals
+ornAna2	mammals
+oryCun2	mammals
+oryLat2	fish
+otoGar3	primates
+oviAri1	mammals
+oviAri3	mammals
+oviAri4	mammals
+panPan1	primates
+panPan2	primates
+panPan3	primates
+panTro1	primates
+panTro2	primates
+panTro3	primates
+panTro4	primates
+panTro5	primates
+panTro6	primates
+papAnu2	primates
+papAnu4	primates
+papHam1	primates
+petMar1	vertebrate
+petMar2	vertebrate
+petMar3	vertebrate
+ponAbe2	primates
+ponAbe3	primates
+priPac1	invertebrate
+proCap1	mammals
+pteVam1	mammals
+rheMac10	primates
+rheMac2	primates
+rheMac3	primates
+rheMac8	primates
+rhiRox1	primates
+rn3	mammals
+rn4	mammals
+rn5	mammals
+rn6	mammals
+rn7	mammals
+sacCer1	fungi
+sacCer2	fungi
+sacCer3	fungi
+saiBol1	primates
+sarHar1	mammals
+sorAra1	mammals
+sorAra2	mammals
+speTri2	mammals
+strPur1	invertebrate
+strPur2	invertebrate
+susScr11	mammals
+susScr2	mammals
+susScr3	mammals
+taeGut1	birds
+taeGut2	birds
+tarSyr1	primates
+tarSyr2	primates
+tetNig1	fish
+tetNig2	fish
+thaSir1	vertebrate
+triMan1	mammals
+tupBel1	mammals
+turTru2	mammals
+vicPac1	mammals
+vicPac2	mammals
+wuhCor1	viral
+xenLae2	vertebrate
+xenTro1	vertebrate
+xenTro10	vertebrate
+xenTro2	vertebrate
+xenTro3	vertebrate
+xenTro7	vertebrate
+xenTro9	vertebrate