0dcda7d7e41d042cdc893034b076b9e70d489af0
hiram
  Wed Sep 11 12:15:48 2019 -0700
fix incorrect name for apaVit1 refs #22687

diff --git src/hg/utils/phyloTrees/commonNames.sh src/hg/utils/phyloTrees/commonNames.sh
index f6a60dc..f651ca0 100755
--- src/hg/utils/phyloTrees/commonNames.sh
+++ src/hg/utils/phyloTrees/commonNames.sh
@@ -1,330 +1,330 @@
 #!/bin/sh
 
 if [ $# -ne 1 ]; then
     echo "usage: ./commonNames.sh <Nway.nh>"
     echo "Renames the names from UCSC database names to common names."
     echo "This depends upon the exact UCSC database names present in the"
     echo ".nh file.  Last updated to work with the 96way.nh file."
     exit 255
 fi
 
 
 export F=$1
 
 /cluster/bin/phast/tree_doctor -r \
 "acaChl1 -> Rifleman ;
 aciJub1 -> Cheetah ;
 ailMel1 -> Panda ;
 allMis1 -> American_alligator ;
 allSin1 -> Chinese_alligator ;
 amaVit1 -> Puerto_Rican_parrot ;
 anaPla1 -> Mallard_duck ;
 ancCey1 -> A__ceylanicum;
 angJap1 -> Japanese_eel ;
 anoCar2 -> Lizard ;
 aotNan1 -> Nancy_Ma_s_night_monkey ;
 apaSpi1 -> Spiny_softshell_turtle ;
-apaVit1 -> Rock_pigeon ;
+apaVit1 -> Bar_tailed_trogon ;
 aptFor1 -> Emperor_penguin ;
 aquChr1 -> Golden_eagle ;
 aquChr2 -> Golden_eagle ;
 araMac1 -> Scarlet_macaw ;
 ascSuu1 -> Pig_roundworm;
 astMex1 -> Mexican_tetra ;
 balAcu1 -> Minke_whale ;
 balPav1 -> Grey_crowned_crain ;
 bisBis1 -> Bison ;
 bosInd1 -> Zebu_cattle ;
 bosMut1 -> Wild_yak ;
 bosTau6 -> Cow ;
 bosTau7 -> Cow ;
 bosTau8 -> Cow ;
 bruMal2 -> Filarial_worm;
 bubBub1 -> Water_buffalo ;
 bucRhi1 -> Rhinoceros_hornbill ;
 burXyl1 -> Pine_wood_nematode;
 caeAng2 -> C__angaria;
 caeJap4 -> C__japonica;
 caePb3 -> C__brenneri;
 caeRem4 -> C__remanei;
 caeSp111 -> C__tropicalis;
 caeSp51 -> C__sp__5_ju800;
 calAnn1 -> Anna_s_hummingbird ;
 calJac3 -> Marmoset ;
 calMil1 -> Elephant_shark ;
 camBac1 -> Bactrian_camel ;
 camDro1 -> Arabian_camel ;
 camFer1 -> Wild_bactrian_camel ;
 canFam2 -> Dog ;
 canFam3 -> Dog ;
 canLup1 -> Gray_wolf ;
 capCar1 -> Chuck_will_s_widow ;
 capHir1 -> Domestic_goat ;
 carCri1 -> Red_legged_seriema ;
 catAur1 -> Turkey_vulture ;
 cavApe1 -> Brazilian_guinea_pig ;
 cavPor3 -> Guinea_pig ;
 cb4 -> C__briggsae;
 ce11 -> C__elegans;
 cebCap1 -> White_faced_sapajou ;
 cerAty1 -> Sooty_mangabey ;
 cerSim1 -> White_rhinoceros ;
 chaPel1 -> Chimney_swift ;
 chaVoc1 -> Killdeer ;
 chaVoc2 -> Killdeer ;
 cheMyd1 -> Green_seaturtle ;
 chiLan1 -> Chinchilla ;
 chlSab1 -> Green_monkey ;
 chlSab2 -> Green_monkey ;
 chlUnd1 -> Macqueen_s_bustard ;
 choHof1 -> Sloth ;
 chrAsi1 -> Cape_golden_mole ;
 chrPic1 -> Painted_turtle ;
 chrPic2 -> Painted_turtle ;
 colAng1 -> Angolan_colobus ;
 colLiv1 -> Rock_pigeon ;
 colStr1 -> Speckled_mousebird ;
 conCri1 -> Star_nosed_mole ;
 corBra1 -> American_crow ;
 corCor1 -> Hooded_crow ;
 cotJap1 -> Japanese_quail ;
 cotJap2 -> Japanese_quail ;
 criGri1 -> Chinese_hamster ;
 croPor1 -> Crocodile ;
 croPor2 -> Crocodile ;
 cucCan1 -> Common_cuckoo ;
 cynSem1 -> Tongue sole ;
 cypVar1 -> Sheepshead_minnow ;
 danRer10 -> Zebrafish ;
 danRer11 -> Zebrafish ;
 danRer7 -> Zebrafish ;
 dasNov2 -> Armadillo ;
 dasNov3 -> Armadillo ;
 dicLab1 -> European_sea_bass ;
 dipOrd1 -> Kangaroo_rat ;
 dipOrd2 -> Kangaroo_rat ;
 dirImm1 -> Dog_heartworm;
 echTel1 -> Tenrec ;
 echTel2 -> Tenrec ;
 egrGar1 -> Little_egret ;
 eidHel1 -> Straw_colored_fruit_bat ;
 eleEdw1 -> Cape_elephant_shrew ;
 eptFus1 -> Big_brown_bat ;
 equAsi1 -> Donkey ;
 equCab2 -> Horse ;
 equPrz1 -> Przewalski_horse ;
 eriEur1 -> Hedgehog ;
 eriEur2 -> Hedgehog ;
 esoLuc1 -> Northern_pike ;
 eulFla1 -> Sclater_s_lemur ;
 eulMac1 -> Black_lemur ;
 eurHel1 -> Sunbittern ;
 falChe1 -> Saker_falcon ;
 falPer1 -> Peregrine_falcon ;
 felCat4 -> Cat ;
 felCat5 -> Cat ;
 felCat8 -> Cat ;
 ficAlb1 -> Collared_flycatcher ;
 ficAlb2 -> Collared_flycatcher ;
 fr2 -> Fugu ;
 fr3 -> Fugu ;
 fukDam1 -> Damara_mole_rat ;
 fulGla1 -> Northern_fulmar ;
 gadMor1 -> Atlantic_cod ;
 galGal3 -> Chicken ;
 galGal4 -> Chicken ;
 galGal5 -> Chicken ;
 galGal6 -> Chicken ;
 galVar1 -> Malayan_flying_lemur ;
 gasAcu1 -> Stickleback ;
 gavGan0 -> Gharial ;
 gavGan1 -> Gharial ;
 gavSte1 -> Red_throated_loon ;
 gekJap1 -> Schlegel_s_Japanese_gecko ;
 geoFor1 -> Medium_ground_finch ;
 gorGor3 -> Gorilla ;
 gorGor5 -> Gorilla ;
 haeCon2 -> Barber_pole_worm;
 halAlb1 -> White_tailed_eagle ;
 halLeu1 -> Bald_eagle ;
 hapBur1 -> Burton_s_mouthbreeder ;
 hetBac1 -> H__bacteriophora/m31e;
 hetGla1 -> Naked_mole_rat ;
 hetGla2 -> Naked_mole_rat ;
 hg19 -> Human ;
 hg38 -> Human ;
 hipArm1 -> Great_roundleaf_bat ;
 jacJac1 -> Lesser_Egyptian_jerboa ;
 latCha1 -> Coelacanth ;
 lepDis1 -> Cuckoo_roller ;
 lepOcu1 -> Spotted_gar ;
 lepWed1 -> Weddell_seal ;
 letCam1 -> Arctic_lamprey ;
 lipVex1 -> Yangtze_river_dolphin ;
 loaLoa1 -> Eye_worm;
 loxAfr3 -> Elephant ;
 macEug2 -> Wallaby ;
 macFas5 -> Crab_eating_macaque ;
 macNem1 -> Pig_tailed_macaque ;
 manJav1 -> Malayan_pangolin ;
 manLeu1 -> Drill ;
 manPen1 -> Chinese_pangolin ;
 manVit1 -> Golden_collared_manakin ;
 manVit2 -> Golden_collared_manakin ;
 marMar1 -> European_marmot ;
 mayZeb1 -> Zebra_mbuna ;
 megLyr1 -> Indian_false_vampire ;
 melGal1 -> Turkey ;
 melGal5 -> Turkey ;
 melHap1 -> M__hapla;
 melInc2 -> M__incognita;
 melUnd1 -> Budgerigar ;
 merNub1 -> Northern_carmine_bee_eater ;
 mesAur1 -> Golden_hamster ;
 mesUni1 -> Brown_roatelo ;
 micMur1 -> Mouse_lemur ;
 micMur3 -> Mouse_lemur ;
 micOch1 -> Prairie_vole ;
 minNat1 -> Natal_long_fingered_bat ;
 mm10 -> Mouse ;
 mm9 -> Mouse ;
 monDom5 -> Opossum ;
 musFur1 -> Ferret ;
 musPut1 -> Ferret ;
 myoBra1 -> Brand_s_bat ;
 myoDav1 -> David_s_myotis ;
 myoLuc1 -> Microbat ;
 myoLuc2 -> Microbat ;
 nanGal1 -> Upper_Galilee_mountains_blind_mole_rat ;
 nanPar1 -> Tibetan_frog ;
 nasLar1 -> Proboscis_monkey ;
 necAme1 -> N__americanus;
 neoBri1 -> Princess_of_Burundi ;
 neoSch1 -> Hawaiian_monk_seal ;
 nesNot1 -> Kea ;
 nipNip1 -> Crested_ibis;
 nomLeu1 -> Gibbon ;
 nomLeu3 -> Gibbon ;
 notCor1 -> Black_rockcod ;
 ochPri2 -> Pika ;
 ochPri3 -> Pika ;
 octDeg1 -> Brush_tailed_rat ;
 odoTex1 -> White_tailed_deer ;
 odoRosDiv1 -> Pacific_walrus ;
 oncVol1 -> O__volvulus;
 opiHoa1 -> Hoatzin ;
 orcOrc1 -> Killer_whale ;
 oreNil1 -> Nile_tilapia ;
 oreNil2 -> Nile_tilapia ;
 oreNil3 -> Nile_tilapia ;
 ornAna1 -> Platypus ;
 ornAna2 -> Platypus ;
 ornAna5 -> Platypus ;
 oryAfe1 -> Aardvark ;
 oryCun2 -> Rabbit ;
 oryLat2 -> Medaka ;
 otoGar1 -> Bushbaby ;
 otoGar3 -> Bushbaby ;
 oviAri1 -> Sheep ;
 oviAri3 -> Sheep ;
 oviMus1 -> Muflon ;
 panHod1 -> Tibetan_antelope ;
 panPan1 -> Bonobo ;
 panPan2 -> Bonobo ;
 panPar1 -> Leopard ;
 panRed1 -> Microworm;
 panTig1 -> Amur_tiger ;
 panTro3 -> Chimp ;
 panTro4 -> Chimp ;
 panTro5 -> Chimp ;
 papAnu2 -> Baboon ;
 papAnu3 -> Baboon ;
 papHam1 -> Baboon ;
 pelCri1 -> Dalmatian_pelican ;
 pelSin1 -> Chinese_softshell_turtle ;
 perManBai1 -> Prairie_deer_mouse ;
 petMar1 -> Lamprey ;
 petMar2 -> Lamprey ;
 petMar3 -> Lamprey ;
 phaCar1 -> Great_cormorant ;
 phaCin1 -> Koala ;
 phaLep1 -> White_tailed_tropicbird ;
 phoRub1 -> American_flamingo ;
 phyCat1 -> Sperm_whale ;
 picPub1 -> Downy_woodpecker ;
 podCri1 -> Great_crested_grebe ;
 poeFor1 -> Amazon_molly ;
 poeRet1 -> Guppy ;
 ponAbe2 -> Orangutan ;
 ponAbe3 -> Orangutan ;
 priExs1 -> P__exspectatus;
 priPac3 -> P__pacificus;
 proCap1 -> Rock_hyrax ;
 proCap2 -> Rock_hyrax ;
 proCoq1 -> Coquerel_s_sifaka ;
 proMuc1 -> Brown_spotted_pit_viper ;
 pseHum1 -> Tibetan_ground_jay ;
 pteAle1 -> Black_flying_fox ;
 pteGut1 -> Yellow_throated_sandgrouse ;
 ptePar1 -> Parnell_s_mustached_bat ;
 pteVam1 -> Megabat ;
 pteVam2 -> Megabat ;
 punNye1 -> Pundamilia_nyererei ;
 pygAde1 -> Adelie_penguin ;
 pytBiv1 -> Burmese_python ;
 rheMac2 -> Rhesus ;
 rheMac3 -> Rhesus ;
 rheMac8 -> Rhesus ;
 rhiBie1 -> Black_snub_nosed_monkey ;
 rhiFer1 -> Greater_horseshoe_bat ;
 rhiRox1 -> Golden_snub_nosed_monkey ;
 rhiSin1 -> Chinese_horseshoe_bat ;
 rn4 -> Rat ;
 rn5 -> Rat ;
 rn6 -> Rat ;
 rouAeg1 -> Egyptian_fruit_bat ;
 saiBol1 -> Squirrel_monkey ;
 sarHar1 -> Tasmanian_devil ;
 sebNig1 -> Tiger_fockfish ;
 sebRub1 -> Flag_fockfish ;
 serCan1 -> Canary ;
 sorAra1 -> Shrew ;
 sorAra2 -> Shrew ;
 speTri1 -> Squirrel ;
 speTri2 -> Squirrel ;
 stePar1 -> Bicolor_damselfish ;
 strCam1 -> Ostrich ;
 strRat2 -> Threadworm;
 susScr2 -> Pig ;
 susScr3 -> Pig ;
 taeGut1 -> Zebra_finch ;
 taeGut2 -> Zebra_finch ;
 takFla1 -> Yellowbelly_pufferfish ;
 tarSyr1 -> Tarsier ;
 tarSyr2 -> Tarsier ;
 tauEry1 -> Red_crested_turaco ;
 tetNig1 -> Tetraodon ;
 tetNig2 -> Tetraodon ;
 thaSir1 -> Garter_snake ;
 tinGut1 -> White_throated_tinamou ;
 tinGut2 -> White_throated_tinamou ;
 triMan1 -> Manatee ;
 triSpi1 -> Trichinella;
 triSui1 -> Whipworm;
 tupBel1 -> Tree_shrew ;
 tupChi1 -> Chinese_tree_shrew ;
 turTru1 -> Dolphin ;
 turTru2 -> Dolphin ;
 tytAlb1 -> Barn_owl ;
 ursMar1 -> Polar_bear ;
 vicPac1 -> Alpaca ;
 vicPac2 -> Alpaca ;
 vipBer1 -> Adder ;
 xenLae2 -> African_clawed_frog ;
 xenTro3 -> Frog_X_tropicalis ;
 xenTro4 -> Frog_X_tropicalis ;
 xenTro7 -> Frog_X_tropicalis ;
 xenTro9 -> Frog_X_tropicalis ;
 xipMac1 -> Southern_platyfish ;
 zonAlb1 -> White_throated_sparrow ;" \
 	${F} | sed -e "s/long_finger/long-finger/; s/rel_s/rel's/; s/Ma_s/Ma's/; s/White_faced/White-faced/; s/White_tailed_deer/White-tailed_deer/; s/Pig_tailed/Pig-tailed/; s/X_trop/X._trop/; s/Burton_s/Burton's/; s/Brand_s/Brand's/; s/David_s/David's/; s/Parnell_s/Parnell's/; s/queen_s/queen's/; s/will_s/will's/; s/Anna_s/Anna's/; s/_nosed/-nosed/; s/00*)/)/g; s/00*,/,/g; s/Schlegel_s/Schlegel's/; s/Sclater_s/Sclater's/"