c036ff920227730eb81df27d750ce6af006d92a5 hiram Wed Oct 7 16:32:54 2020 -0700 cleaning up stray chainNet tracks outside composites refs #22271 diff --git src/hg/makeDb/trackDb/human/chainNetPlacental.ra src/hg/makeDb/trackDb/human/chainNetPlacental.ra index 275170b..aaff79b 100644 --- src/hg/makeDb/trackDb/human/chainNetPlacental.ra +++ src/hg/makeDb/trackDb/human/chainNetPlacental.ra @@ -1,21 +1,21 @@ track placentalChainNet compositeTrack on shortLabel Placental Chain/Net longLabel Non-primate Placental Mammal Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets -subGroup2 species Species s000=Guinea_pig s001=Guinea_pig s002=Chinchilla s003=Chinese_hamster s004a=Chinese_hamster_CHOv1 s004b=Chinese_hamster_CHOv2 s004c=RegenCHO1 s005a=Kangaroo_rat s005b=Beaver s006=Malayan_flying_lemur s007=Naked_mole-rat s008=Naked_mole-rat s0081=Damara_mole-rat s009=Lesser_Egyptian_jerboa s010=Golden_hamster s011=Prairie_vole s012a=Mouse s012b=Mouse38B s012c=Mouse s013=Mouse s014=Mouse s015=Mouse s016=Mouse s017=Upper_Galilee_mountains_blind_mole_rat s018=Pika s019=Pika s020=Brush-tailed_rat s021=Rabbit s022=Rabbit s023=Prairie_deer_mouse s024=Rat s025=Rat s026=Rat s027=Rat s028=Rat s029=Squirrel s030=Squirrel s031=Tree_shrew s032=Chinese_tree_shrew s033=Panda s034a=Dog s034b=Dog s035=Dog s036=Dog s037=Dog s037b=Cat s038=Cat s039=Cat s040=Cat s041=Cat s042=Weddell_seal s043=Ferret s043a=Southern_sea_otter s044=Hawaiian_monk_seal s045=Pacific_walrus s046=Amur_tiger s047=Polar_bear s048=Minke_whale s049=Bison s050=Wild_yak s051a=Cow s051b=Cow s052=Cow s053=Cow s054=Cow s055=Cow s056=Cow s057=Cow s058=Cow s059=Cow s060=Water_buffalo s061=Bactrian_camel s062=Domestic_goat s063=Yangtze_river_dolphin s064=Killer_whale s065a=Sheep s065b=Sheep s065c=Sheep s067=Tibetan_antelope s068=Sperm_whale s069=Pig s070=Pig s071=Pig s072=Pig s073=Dolphin s074=Dolphin s075=Alpaca s076=Alpaca s077=Straw_colored_fruit_bat s078=Big_brown_bat s079=Indian_false_vampire s080=Brandt's_myotis_(bat) s081=David's_myotis_(bat) s082=Microbat s083=Microbat s084=Black_flying-fox s085=Parnell's_mustached_bat s086=Megabat s087=Greater_horseshoe_bat s088=Egyptian_rousette s089=Star-nosed_mole s090=Hedgehog s091=Hedgehog s092=Chinese_pangolin s093=Shrew s094=Shrew s095=White_rhinoceros s096a=Horse s096b=Horse s096c=Horse s098=Przewalski_horse s099=Sloth s100=Armadillo s101=Armadillo s102=Armadillo s103=Cape_golden_mole s104=Tenrec s105=Tenrec s106=Cape_elephant_shrew s107=Elephant s108=Elephant s109=Elephant s110=Aardvark s111=Rock_hyrax s112=Manatee +subGroup2 species Species s000=Guinea_pig s001=Guinea_pig s002=Chinchilla s003=Chinese_hamster s004a=Chinese_hamster_CHOv1 s004b=Chinese_hamster_CHOv2 s004c=RegenCHO1 s005a=Kangaroo_rat s005b=Beaver s006=Malayan_flying_lemur s007=Naked_mole-rat s008=Naked_mole-rat s0081=Damara_mole-rat s009=Lesser_Egyptian_jerboa s010=Golden_hamster s011=Prairie_vole s012a=Mouse s012b=Mouse38B s012c=Mouse s013=Mouse s014=Mouse s015=Mouse s016=Mouse s017=Upper_Galilee_mountains_blind_mole_rat s018=Pika s019=Pika s020=Brush-tailed_rat s021=Rabbit s022=Rabbit s023=Prairie_deer_mouse s024a=RegenRn1 s024b=RegenRn0 s024c=Rat s025=Rat s026=Rat s027=Rat s028=Rat s029=Squirrel s030=Squirrel s031=Tree_shrew s032=Chinese_tree_shrew s033=Panda s034a=Dog s034b=Dog s034c=Dog s035=Dog s036=Dog s037=Dog s037b=Cat s038=Cat s039=Cat s040=Cat s041=Cat s042=Weddell_seal s043=Ferret s043a=Southern_sea_otter s044=Hawaiian_monk_seal s045=Pacific_walrus s046=Amur_tiger s047=Polar_bear s048=Minke_whale s049=Bison s050=Wild_yak s051a=Cow s051b=Cow s052=Cow s053=Cow s054=Cow s055=Cow s056=Cow s057=Cow s058=Cow s059=Cow s060=Water_buffalo s061=Bactrian_camel s062=Domestic_goat s063=Yangtze_river_dolphin s064=Killer_whale s065a=Sheep s065b=Sheep s065c=Sheep s067=Tibetan_antelope s068=Sperm_whale s069=Pig s070=Pig s071=Pig s072=Pig s073=Dolphin s074=Dolphin s075=Alpaca s076=Alpaca s077=Straw_colored_fruit_bat s078=Big_brown_bat s079=Indian_false_vampire s080=Brandt's_myotis_(bat) s081=David's_myotis_(bat) s082=Microbat s083=Microbat s084=Black_flying-fox s085=Parnell's_mustached_bat s086=Megabat s087=Greater_horseshoe_bat s088=Egyptian_rousette s089=Star-nosed_mole s090=Hedgehog s091=Hedgehog s092=Chinese_pangolin s093=Shrew s094=Shrew s095=White_rhinoceros s096a=Horse s096b=Horse s096c=Horse s098=Przewalski_horse s099=Sloth s100=Armadillo s101=Armadillo s102=Armadillo s103=Cape_golden_mole s104=Tenrec s105=Tenrec s106=Cape_elephant_shrew s107=Elephant s108=Elephant s109=Elephant s110=Aardvark s111=Rock_hyrax s112=Manatee subGroup3 clade Clade c00=Euarchontoglires c01=Carnivora c02=Cetartiodactyla c03=Chiroptera c04=Laurasiatheria c05=Perissodactyla c06=Xenarthra c07=Afrotheria dragAndDrop subTracks visibility hide group compGeno noInherit on color 0,0,0 altColor 255,255,0 type bed 3 chainLinearGap loose chainMinScore 5000 dimensions dimensionX=clade dimensionY=species sortOrder species=+ view=+ clade=+ configurable on html placentalChainNet priority 8 @@ -263,33 +263,49 @@ subTrack placentalChainNetViewchain off subGroups view=chain species=s022 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain oryCun1 otherDb oryCun1 track chainPerManBai1 subTrack placentalChainNetViewchain off subGroups view=chain species=s023 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain perManBai1 otherDb perManBai1 + track chainRegenRn1 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s024a clade=c00 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain RegenRn1 + otherDb regenRn1 + + track chainRegenRn0 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s024b clade=c00 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain RegenRn0 + otherDb regenRn0 + track chainRn6 subTrack placentalChainNetViewchain off - subGroups view=chain species=s024 clade=c00 + subGroups view=chain species=s024c clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rn6 otherDb rn6 track chainRn5 subTrack placentalChainNetViewchain off subGroups view=chain species=s025 clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rn5 otherDb rn5 track chainRn4 subTrack placentalChainNetViewchain off @@ -343,41 +359,49 @@ subTrack placentalChainNetViewchain off subGroups view=chain species=s032 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain tupChi1 otherDb tupChi1 track chainAilMel1 subTrack placentalChainNetViewchain off subGroups view=chain species=s033 clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain ailMel1 otherDb ailMel1 - track chainCanFam4 + track chainCanFam5 subTrack placentalChainNetViewchain off subGroups view=chain species=s034a clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments + type chain canFam5 + otherDb canFam5 + + track chainCanFam4 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s034b clade=c01 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments type chain canFam4 otherDb canFam4 track chainCanFam3 subTrack placentalChainNetViewchain off - subGroups view=chain species=s034b clade=c01 + subGroups view=chain species=s034c clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain canFam3 otherDb canFam3 track chainCanFam2 subTrack placentalChainNetViewchain off subGroups view=chain species=s035 clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain canFam2 otherDb canFam2 track chainCanFam1 subTrack placentalChainNetViewchain off @@ -1277,33 +1301,49 @@ subTrack placentalChainNetViewnet off subGroups view=net species=s022 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign oryCun1 chainOryCun1 otherDb oryCun1 track netPerManBai1 subTrack placentalChainNetViewnet off subGroups view=net species=s023 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign perManBai1 chainPerManBai1 otherDb perManBai1 + track netRegenRn1 + subTrack placentalChainNetViewnet on + subGroups view=net species=s024a clade=c00 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign regenRn1 chainRegenRn1 + otherDb regenRn1 + + track netRegenRn0 + subTrack placentalChainNetViewnet on + subGroups view=net species=s024b clade=c00 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign regenRn0 chainRegenRn0 + otherDb regenRn0 + track netRn6 subTrack placentalChainNetViewnet on - subGroups view=net species=s024 clade=c00 + subGroups view=net species=s024c clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rn6 chainRn6 otherDb rn6 track netRn5 subTrack placentalChainNetViewnet off subGroups view=net species=s025 clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rn5 chainRn5 otherDb rn5 track netRn4 subTrack placentalChainNetViewnet off @@ -1357,41 +1397,49 @@ subTrack placentalChainNetViewnet off subGroups view=net species=s032 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign tupChi1 chainTupChi1 otherDb tupChi1 track netAilMel1 subTrack placentalChainNetViewnet off subGroups view=net species=s033 clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign ailMel1 chainAilMel1 otherDb ailMel1 - track netCanFam4 + track netCanFam5 subTrack placentalChainNetViewnet on subGroups view=net species=s034a clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net + type netAlign canFam5 chainCanFam5 + otherDb canFam5 + + track netCanFam4 + subTrack placentalChainNetViewnet on + subGroups view=net species=s034b clade=c01 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net type netAlign canFam4 chainCanFam4 otherDb canFam4 track netCanFam3 subTrack placentalChainNetViewnet on - subGroups view=net species=s034b clade=c01 + subGroups view=net species=s034c clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign canFam3 chainCanFam3 otherDb canFam3 track netCanFam2 subTrack placentalChainNetViewnet off subGroups view=net species=s035 clade=c01 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign canFam2 chainCanFam2 otherDb canFam2 track netCanFam1 subTrack placentalChainNetViewnet off