Association table of common names and assembly identifiers in the 100-vertebrate genome alignments from UCSC Genome Browser

commonNames_assemblies.semijson

["Human","hg19"],
["Chimp","panTro4"],
["Gorilla","gorGor3"],
["Orangutan","ponAbe2"],
["Gibbon","nomLeu3"],
["Rhesus","rheMac3"],
["Crab_eating_macaque","macFas5"],
["Baboon","papHam1"],
["Green_monkey","chlSab1"],
["Marmoset","calJac3"],
["Squirrel_monkey","saiBol1"],
["Bushbaby","otoGar3"],
["Chinese_tree_shrew","tupChi1"],
["Squirrel","speTri2"],
["Lesser_Egyptian_jerboa","jacJac1"],
["Prairie_vole","micOch1"],
["Chinese_hamster","criGri1"],
["Golden_hamster","mesAur1"],
["Mouse","mm10"],
["Rat","rn5"],
["Naked_mole_rat","hetGla2"],
["Guinea_pig","cavPor3"],
["Chinchilla","chiLan1"],
["Brush_tailed_rat","octDeg1"],
["Rabbit","oryCun2"],
["Pika","ochPri3"],
["Pig","susScr3"],
["Alpaca","vicPac2"],
["Bactrian_camel","camFer1"],
["Dolphin","turTru2"],
["Killer_whale","orcOrc1"],
["Tibetan_antelope","panHod1"],
["Cow","bosTau7"],
["Sheep","oviAri3"],
["Domestic_goat","capHir1"],
["Horse","equCab2"],
["White_rhinoceros","cerSim1"],
["Cat","felCat5"],
["Dog","canFam3"],
["Ferret","musFur1"],
["Panda","ailMel1"],
["Pacific_walrus","odoRosDiv1"],
["Weddell_seal","lepWed1"],
["Black_flying_fox","pteAle1"],
["Megabat","pteVam1"],
["David's_myotis","myoDav1"],
["Microbat","myoLuc2"],
["Big_brown_bat","eptFus1"],
["Hedgehog","eriEur2"],
["Shrew","sorAra2"],
["Star-nosed_mole","conCri1"],
["Elephant","loxAfr3"],
["Cape_elephant_shrew","eleEdw1"],
["Manatee","triMan1"],
["Cape_golden_mole","chrAsi1"],
["Tenrec","echTel2"],
["Aardvark","oryAfe1"],
["Armadillo","dasNov3"],
["Opossum","monDom5"],
["Tasmanian_devil","sarHar1"],
["Wallaby","macEug2"],
["Platypus","ornAna1"],
["Saker_falcon","falChe1"],
["Peregrine_falcon","falPer1"],
["Collared_flycatcher","ficAlb2"],
["White_throated_sparrow","zonAlb1"],
["Medium_ground_finch","geoFor1"],
["Zebra_finch","taeGut2"],
["Tibetan_ground_jay","pseHum1"],
["Budgerigar","melUnd1"],
["Puerto_Rican_parrot","amaVit1"],
["Scarlet_macaw","araMac1"],
["Rock_pigeon","colLiv1"],
["Mallard_duck","anaPla1"],
["Chicken","galGal4"],
["Turkey","melGal1"],
["American_alligator","allMis1"],
["Green_seaturtle","cheMyd1"],
["Painted_turtle","chrPic1"],
["Chinese_softshell_turtle","pelSin1"],
["Spiny_softshell_turtle","apaSpi1"],
["Lizard","anoCar2"],
["Frog_X._tropicalis","xenTro7"],
["Coelacanth","latCha1"],
["Tetraodon","tetNig2"],
["Fugu","fr3"],
["Yellowbelly_pufferfish","takFla1"],
["Nile_tilapia","oreNil2"],
["Princess_of_Burundi","neoBri1"],
["Burton's_mouthbreeder","hapBur1"],
["Zebra_mbuna","mayZeb1"],
["Pundamilia_nyererei","punNye1"],
["Medaka","oryLat2"],
["Southern_platyfish","xipMac1"],
["Stickleback","gasAcu1"],
["Atlantic_cod","gadMor1"],
["Zebrafish","danRer7"],
["Mexican_tetra","astMex1"],
["Spotted_gar","lepOcu1"],
["Lamprey","petMar2"],

commonNames_assemblies.txt

Human	hg19
Chimp	panTro4
Gorilla	gorGor3
Orangutan	ponAbe2
Gibbon	nomLeu3
Rhesus	rheMac3
Crab_eating_macaque	macFas5
Baboon	papHam1
Green_monkey	chlSab1
Marmoset	calJac3
Squirrel_monkey	saiBol1
Bushbaby	otoGar3
Chinese_tree_shrew	tupChi1
Squirrel	speTri2
Lesser_Egyptian_jerboa	jacJac1
Prairie_vole	micOch1
Chinese_hamster	criGri1
Golden_hamster	mesAur1
Mouse	mm10
Rat	rn5
Naked_mole_rat	hetGla2
Guinea_pig	cavPor3
Chinchilla	chiLan1
Brush_tailed_rat	octDeg1
Rabbit	oryCun2
Pika	ochPri3
Pig	susScr3
Alpaca	vicPac2
Bactrian_camel	camFer1
Dolphin	turTru2
Killer_whale	orcOrc1
Tibetan_antelope	panHod1
Cow	bosTau7
Sheep	oviAri3
Domestic_goat	capHir1
Horse	equCab2
White_rhinoceros	cerSim1
Cat	felCat5
Dog	canFam3
Ferret	musFur1
Panda	ailMel1
Pacific_walrus	odoRosDiv1
Weddell_seal	lepWed1
Black_flying_fox	pteAle1
Megabat	pteVam1
David's_myotis	myoDav1
Microbat	myoLuc2
Big_brown_bat	eptFus1
Hedgehog	eriEur2
Shrew	sorAra2
Star-nosed_mole	conCri1
Elephant	loxAfr3
Cape_elephant_shrew	eleEdw1
Manatee	triMan1
Cape_golden_mole	chrAsi1
Tenrec	echTel2
Aardvark	oryAfe1
Armadillo	dasNov3
Opossum	monDom5
Tasmanian_devil	sarHar1
Wallaby	macEug2
Platypus	ornAna1
Saker_falcon	falChe1
Peregrine_falcon	falPer1
Collared_flycatcher	ficAlb2
White_throated_sparrow	zonAlb1
Medium_ground_finch	geoFor1
Zebra_finch	taeGut2
Tibetan_ground_jay	pseHum1
Budgerigar	melUnd1
Puerto_Rican_parrot	amaVit1
Scarlet_macaw	araMac1
Rock_pigeon	colLiv1
Mallard_duck	anaPla1
Chicken	galGal4
Turkey	melGal1
American_alligator	allMis1
Green_seaturtle	cheMyd1
Painted_turtle	chrPic1
Chinese_softshell_turtle	pelSin1
Spiny_softshell_turtle	apaSpi1
Lizard	anoCar2
Frog_X._tropicalis	xenTro7
Coelacanth	latCha1
Tetraodon	tetNig2
Fugu	fr3
Yellowbelly_pufferfish	takFla1
Nile_tilapia	oreNil2
Princess_of_Burundi	neoBri1
Burton's_mouthbreeder	hapBur1
Zebra_mbuna	mayZeb1
Pundamilia_nyererei	punNye1
Medaka	oryLat2
Southern_platyfish	xipMac1
Stickleback	gasAcu1
Atlantic_cod	gadMor1
Zebrafish	danRer7
Mexican_tetra	astMex1
Spotted_gar	lepOcu1
Lamprey	petMar2

munge.sh

#!/bin/bash -ex

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz100way/hg19.100way.commonNames.nh
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz100way/hg19.100way.nh
cat hg19.100way.commonNames.nh | tr -d '();, ' | cut -d ':' -f1 > commonNames.txt
cat hg19.100way.nh | tr -d '();, ' | cut -d ':' -f1 > assemblies.txt
paste commonNames.txt assemblies.txt > commonNames_assemblies.txt
cat commonNames_assemblies.txt | awk '{printf("[\"%s\",\"%s\"],\n",$1,$2)}' > commonNames_assemblies.semijson