08b3b394e57c1ca8a8b31ad773e2e7506c32b56b hiram Wed Oct 7 15:06:28 2020 -0700 package in mm39 chainNet properly and a couple others refs #22271 diff --git src/hg/makeDb/trackDb/human/chainNetPlacental.ra src/hg/makeDb/trackDb/human/chainNetPlacental.ra index 537a92e..275170b 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 s004=Chinese_hamster_CHOv1 s0045=Chinese_hamster_CHOv2 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 s012=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 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 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 @@ -49,44 +49,52 @@ shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain chiLan1 otherDb chiLan1 track chainCriGri1 subTrack placentalChainNetViewchain off subGroups view=chain species=s003 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain criGri1 otherDb criGri1 track chainCriGriChoV1 subTrack placentalChainNetViewchain off - subGroups view=chain species=s004 clade=c00 + subGroups view=chain species=s004a clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain criGriChoV1 otherDb criGriChoV1 track chainCriGriChoV2 subTrack placentalChainNetViewchain off - subGroups view=chain species=s0045 clade=c00 + subGroups view=chain species=s004b clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain criGriChoV2 otherDb criGriChoV2 + track chainRegenCho1 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s004c clade=c00 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain regenCho1 + otherDb regenCho1 + track chainDipOrd2 subTrack placentalChainNetViewchain off subGroups view=chain species=s005a clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain dipOrd2 otherDb dipOrd2 track chainDipOrd1 subTrack placentalChainNetViewchain off subGroups view=chain species=s005a clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain dipOrd1 otherDb dipOrd1 @@ -143,33 +151,49 @@ subTrack placentalChainNetViewchain off subGroups view=chain species=s010 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain mesAur1 otherDb mesAur1 track chainMicOch1 subTrack placentalChainNetViewchain off subGroups view=chain species=s011 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain micOch1 otherDb micOch1 + track chainMm39 + subTrack placentalChainNetViewchain off + subGroups view=chain species=s012a clade=c00 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain mm39 + otherDb mm39 + + track chainGRCm38B + subTrack placentalChainNetViewchain off + subGroups view=chain species=s012b clade=c00 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain GRCm38B + otherDb GRCm38B + track chainMm10 subTrack placentalChainNetViewchain off - subGroups view=chain species=s012 clade=c00 + subGroups view=chain species=s012c clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain mm10 otherDb mm10 track chainMm9 subTrack placentalChainNetViewchain off subGroups view=chain species=s013 clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain mm9 otherDb mm9 track chainMm8 subTrack placentalChainNetViewchain off @@ -1039,44 +1063,52 @@ shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign chiLan1 chainChiLan1 otherDb chiLan1 track netCriGri1 subTrack placentalChainNetViewnet off subGroups view=net species=s003 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign criGri1 chainCriGri1 otherDb criGri1 track netCriGriChoV1 subTrack placentalChainNetViewnet off - subGroups view=net species=s004 clade=c00 + subGroups view=net species=s004a clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign criGriChoV1 chainCriGriChoV1 otherDb criGriChoV1 track netCriGriChoV2 subTrack placentalChainNetViewnet off - subGroups view=net species=s0045 clade=c00 + subGroups view=net species=s004b clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign criGriChoV2 chainCriGriChoV2 otherDb criGriChoV2 + track netRegenCho1 + subTrack placentalChainNetViewnet off + subGroups view=net species=s004c clade=c00 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign criGriRegenCho1 chainRegenCho1 + otherDb regenCho1 + track netDipOrd2 subTrack placentalChainNetViewnet off subGroups view=net species=s005a clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign dipOrd2 chainDipOrd2 otherDb dipOrd2 track netDipOrd1 subTrack placentalChainNetViewnet off subGroups view=net species=s005a clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign dipOrd1 chainDipOrd1 otherDb dipOrd1 @@ -1133,33 +1165,49 @@ subTrack placentalChainNetViewnet off subGroups view=net species=s010 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign mesAur1 chainMesAur1 otherDb mesAur1 track netMicOch1 subTrack placentalChainNetViewnet off subGroups view=net species=s011 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign micOch1 chainMicOch1 otherDb micOch1 + track netMm39 + subTrack placentalChainNetViewnet on + subGroups view=net species=s012a clade=c00 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign mm39 chainMm39 + otherDb mm39 + + track netGRCm38B + subTrack placentalChainNetViewnet on + subGroups view=net species=s012b clade=c00 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign GRCm38B chainGRCm38B + otherDb GRCm38B + track netMm10 subTrack placentalChainNetViewnet on - subGroups view=net species=s012 clade=c00 + subGroups view=net species=s012c clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign mm10 chainMm10 otherDb mm10 track netMm9 subTrack placentalChainNetViewnet off subGroups view=net species=s013 clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign mm9 chainMm9 otherDb mm9 track netMm8 subTrack placentalChainNetViewnet off