253725f97da38e647a3f7ac58043a0022b1c4847 hiram Thu Feb 9 15:00:07 2023 -0800 bring in Asiatic elephant, domestic cat, and platypus GenArk hub chain tracks into composite refs #30555 diff --git src/hg/makeDb/trackDb/human/chainNetVertebrate.ra src/hg/makeDb/trackDb/human/chainNetVertebrate.ra index 1553653..2e60f75 100644 --- src/hg/makeDb/trackDb/human/chainNetVertebrate.ra +++ src/hg/makeDb/trackDb/human/chainNetVertebrate.ra @@ -1,21 +1,21 @@ track vertebrateChainNet compositeTrack on shortLabel Vertebrate Chain/Net longLabel Non-placental Vertebrate Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets -subGroup2 species Species s000=Wallaby s001=Wallaby s002=Tasmanian_devil s003=Opossum s004=Platypus s005=Platypus s006=Turkey s007a=Turkey s007b=Japanese_quail s008a=Chicken s008b=Chicken s009=Chicken s010=Chicken s011=Mallard_duck s012=Scarlet_macaw s013=Medium_ground_finch s014=White-throated_sparrow s015=Collared_flycatcher s016=Golden_eagle s017=Peregrine_falcon s018=Saker_falcon s019=Rock_pigeon s020=Parrot s021=Budgerigar s022=Tibetan_ground_jay s023=Zebra_finch s024=Zebra_finch s025=American_alligator s026=Chinese_alligator s027=Lizard s028=Lizard s028b=Garter_snake s029a=Axolotl s029b=X._tropicalis s029c=X._tropicalis s030=X._tropicalis s031=X._tropicalis s032=X._tropicalis s033=X._tropicalis s034=African_clawed_frog s035=Spiny_softshell_turtle s036=Chinese_softshell_turtle s037=Painted_turtle s038=Painted_turtle s039=Green_seaturtle s040=Coelacanth s041=Spotted_gar s042=Mexican_tetra_(cavefish) s043=Zebrafish s044=Zebrafish s045=Zebrafish s046=Zebrafish s047=Zebrafish s048=Atlantic_cod s049=Stickleback s050=Southern_platyfish s051=Medaka s052=Pundamilia_nyererei s053=Zebra_mbuna s054=Princess_of_Burundi s055=Burton's_mouthbreeder s056=Nile_tilapia s057=Nile_tilapia s058=Nile_tilapia s059=Yellowbelly_pufferfish s060=Fugu s061=Fugu s062=Tetraodon s063=Tetraodon s064a=Lamprey s064b=Lamprey s065=Lamprey s066=Arctic_lamprey +subGroup2 species Species s000=Wallaby s001=Wallaby s002=Tasmanian_devil s003=Opossum s004a=Platypus s004b=Platypus s005=Platypus s006=Turkey s007a=Turkey s007b=Japanese_quail s008a=Chicken s008b=Chicken s009=Chicken s010=Chicken s011=Mallard_duck s012=Scarlet_macaw s013=Medium_ground_finch s014=White-throated_sparrow s015=Collared_flycatcher s016=Golden_eagle s017=Peregrine_falcon s018=Saker_falcon s019=Rock_pigeon s020=Parrot s021=Budgerigar s022=Tibetan_ground_jay s023=Zebra_finch s024=Zebra_finch s025=American_alligator s026=Chinese_alligator s027=Lizard s028=Lizard s028b=Garter_snake s029a=Axolotl s029b=X._tropicalis s029c=X._tropicalis s030=X._tropicalis s031=X._tropicalis s032=X._tropicalis s033=X._tropicalis s034=African_clawed_frog s035=Spiny_softshell_turtle s036=Chinese_softshell_turtle s037=Painted_turtle s038=Painted_turtle s039=Green_seaturtle s040=Coelacanth s041=Spotted_gar s042=Mexican_tetra_(cavefish) s043=Zebrafish s044=Zebrafish s045=Zebrafish s046=Zebrafish s047=Zebrafish s048=Atlantic_cod s049=Stickleback s050=Southern_platyfish s051=Medaka s052=Pundamilia_nyererei s053=Zebra_mbuna s054=Princess_of_Burundi s055=Burton's_mouthbreeder s056=Nile_tilapia s057=Nile_tilapia s058=Nile_tilapia s059=Yellowbelly_pufferfish s060=Fugu s061=Fugu s062=Tetraodon s063=Tetraodon s064a=Lamprey s064b=Lamprey s065=Lamprey s066=Arctic_lamprey subGroup3 clade Clade c00=mammalia c01=dinosauria c02=lepidosauria c03=amphibia c04=cryptodira c05=coelancanthimorpha c06=neopterygii c07=hyperoartia 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 vertebrateChainNet priority 9 @@ -47,33 +47,43 @@ subTrack vertebrateChainNetViewchain off subGroups view=chain species=s002 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain sarHar1 otherDb sarHar1 track chainMonDom5 subTrack vertebrateChainNetViewchain off subGroups view=chain species=s003 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain monDom5 otherDb monDom5 + track chainGCF_004115215.2 + subTrack vertebrateChainNetViewchain off + subGroups view=chain species=s004a clade=c00 + shortLabel Platypus Chain + longLabel Platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Chained Alignments + type bigChain GCF_004115215.2 + bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_004115215.2.bb + linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_004115215.2Link.bb + otherDb GCF_004115215.2 + track chainOrnAna2 subTrack vertebrateChainNetViewchain off - subGroups view=chain species=s004 clade=c00 + subGroups view=chain species=s004b clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain ornAna2 otherDb ornAna2 track chainOrnAna1 subTrack vertebrateChainNetViewchain off subGroups view=chain species=s005 clade=c00 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain ornAna1 otherDb ornAna1 track chainMelGal5 subTrack vertebrateChainNetViewchain off @@ -637,33 +647,45 @@ subTrack vertebrateChainNetViewnet off subGroups view=net species=s002 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign sarHar1 chainSarHar1 otherDb sarHar1 track netMonDom5 subTrack vertebrateChainNetViewnet on subGroups view=net species=s003 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign monDom5 chainMonDom5 otherDb monDom5 + track netGCF_004115215.2 + subTrack vertebrateChainNetViewnet off + subGroups view=net species=s004a clade=c00 + shortLabel Platypus Net + longLabel Platypus (Nov. 2020 GCF_004115215.2_mOrnAna1.pri.v4) Net Alignment + type bigMaf + bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.net.bb + summary /gbdb/$D/bbi/chainNet/$D.GCF_004115215.2.net.summary.bb + speciesOrder GCF_004115215.2 + speciesLabels GCF_004115215.2="Platypus" + otherDb GCF_004115215.2 + track netOrnAna2 subTrack vertebrateChainNetViewnet off - subGroups view=net species=s004 clade=c00 + subGroups view=net species=s004b clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign ornAna2 chainOrnAna2 otherDb ornAna2 track netOrnAna1 subTrack vertebrateChainNetViewnet off subGroups view=net species=s005 clade=c00 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign ornAna1 chainOrnAna1 otherDb ornAna1 track netMelGal5 subTrack vertebrateChainNetViewnet off