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Created December 2, 2013 05:11
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Association table of common names and assembly identifiers in the 100-vertebrate genome alignments from UCSC Genome Browser
["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"],
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
#!/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
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