src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.1
1.1 2009/12/07 22:00:51 hiram
Move all the chainNet definitions off to their own file
Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: src/hg/makeDb/trackDb/trackDb.chainNet.ra
diff -N src/hg/makeDb/trackDb/trackDb.chainNet.ra
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra 7 Dec 2009 22:00:51 -0000 1.1
@@ -0,0 +1,559 @@
+# "$Id$";
+
+# release alpha until individual fr2 tracks are obsolete
+track chainNetFr2
+release alpha
+compositeTrack on
+shortLabel Fugu Chain/Net
+longLabel Fugu (Oct. 2004/fr2), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 159
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb fr2
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+ track chainFr2
+ release alpha
+ subTrack chainNetFr2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain fr2
+
+ track netFr2
+ release alpha
+ subTrack chainNetFr2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign fr2 chainFr2
+
+track chainNetTetNig2
+compositeTrack on
+shortLabel Tetraodon Chain/Net
+longLabel Tetraodon (Mar. 2007/tetNig2), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 159
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb tetNig2
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+ track chainTetNig2
+ subTrack chainNetTetNig2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain tetNig2
+
+ track netTetNig2
+ subTrack chainNetTetNig2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign tetNig2 chainTetNig2
+
+track chainNetDanRer6
+compositeTrack on
+shortLabel Zebrafish Chain/Net
+longLabel Zebrafish (Dec. 2008/danRer6), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 159
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb danRer6
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+ track chainDanRer6
+ subTrack chainNetDanRer6
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain danRer6
+
+ track netDanRer6
+ subTrack chainNetDanRer6
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign danRer6 chainDanRer6
+
+# release alpha until individual oryLat2 tracks are obsolete
+track chainNetOryLat2
+release alpha
+compositeTrack on
+shortLabel Medaka Chain/Net
+longLabel Medaka (Oct. 2005/oryLat2), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 165.5
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb hg19
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+ track chainOryLat2
+ release alpha
+ subTrack chainNetOryLat2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain oryLat2
+ otherDb oryLat2
+
+ track netOryLat2
+ release alpha
+ subTrack chainNetOryLat2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign oryLat2 chainOryLat2
+ otherDb oryLat2
+
+# release alpha until individual gasAcu1 tracks are obsolete
+track chainNetGasAcu1
+compositeTrack on
+shortLabel Stickleback Chain/Net
+longLabel Stickleback (Feb 2006/gasAcu1), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 181
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb gasAcu1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainGasAcu1
+ release alpha
+ subTrack chainNetGasAcu1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain gasAcu1
+
+ track netGasAcu1
+ release alpha
+ subTrack chainNetGasAcu1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign gasAcu1 chainGasAcu1
+
+# release alpha until individual galGal3 tracks are obsolete
+track chainNetGalGal3
+compositeTrack on
+shortLabel Chicken Chain/Net
+longLabel Chicken (May 2006/galGal3), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 181
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb galGal3
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainGalGal3
+ release alpha
+ subTrack chainNetGalGal3
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain galGal3
+
+ track netGalGal3
+ release alpha
+ subTrack chainNetGalGal3
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign galGal3 chainGalGal3
+
+# release alpha until ornAna1 individual chain/net tracks phased out
+track chainNetOrnAna1
+compositeTrack on
+shortLabel Platypus Chain/Net
+longLabel Platypus (Mar. 2007/ornAna1), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 191
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb ornAna1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainOrnAna1
+ release alpha
+ subTrack chainNetOrnAna1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain ornAna1
+
+ track netOrnAna1
+ release alpha
+ subTrack chainNetOrnAna1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign ornAna1 chainOrnAna1
+
+track chainNetMonDom5
+compositeTrack on
+shortLabel Opossum Chain/Net
+longLabel Opossum (Oct. 2006/monDom5), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 191
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb monDom5
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainMonDom5
+ subTrack chainNetMonDom5
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain monDom5
+
+ track netMonDom5
+ subTrack chainNetMonDom5
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign monDom5 chainMonDom5
+
+# release alpha until mm9 individual chain/net tracks phased out
+track chainNetMm9
+compositeTrack on
+shortLabel Mouse Chain/Net
+longLabel Mouse (Jul. 2007/mm9), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb mm9
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainMm9
+ release alpha
+ subTrack chainNetMm9
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain mm9
+
+ track netMm9
+ release alpha
+ subTrack chainNetMm9
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign mm9 chainMm9
+
+track chainNetEquCab2
+compositeTrack on
+shortLabel Horse Chain/Net
+longLabel Horse (Sep. 2007/equCab2), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 240
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb equCab2
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainEquCab2
+ subTrack chainNetEquCab2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain equCab2
+
+ track netEquCab2
+ subTrack chainNetEquCab2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign equCab2 chainEquCab2
+
+# release alpha until canFam2 individual tracks phased out
+track chainNetCanFam2
+compositeTrack on
+shortLabel Dog Chain/Net
+longLabel Dog (May 2005/canFam2), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 240
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb canFam2
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainCanFam2
+ release alpha
+ subTrack chainNetCanFam2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain canFam2
+
+ track netCanFam2
+ release alpha
+ subTrack chainNetCanFam2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign canFam2 chainCanFam2
+
+track chainNetVenter
+compositeTrack on
+shortLabel Venter Chain/Net
+longLabel J. Craig Venter Chain and Net Alignments
+subGroup1 view Views chain=Chains net=Nets
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 500
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+
+ track chainVenter1
+ subTrack chainNetVenter off
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ color 100,50,0
+ altColor 255,240,200
+ matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+ matrixHeader A, C, G, T
+ type chain venter1
+ otherDb venter1
+
+ track netVenter1
+ subTrack chainNetVenter off
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign venter1 chainVenter1
+ otherDb venter1
+
+track chainNetHg19
+compositeTrack on
+shortLabel Human Chain/Net
+longLabel Human (Feb. 2009/hg19), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 498
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
+matrixHeader A, C, G, T
+otherDb hg19
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+ track chainHg19
+ subTrack chainNetHg19
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain hg19
+
+ track netHg19
+ subTrack chainNetHg19
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment net
+ type netAlign hg19 chainHg19
+
+track chainNetPoodle
+compositeTrack on
+shortLabel Poodle Chain/Net
+longLabel Poodle Chain and Net Alignments
+subGroup1 view Views chain=Chains net=Nets
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 500
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+
+ track chainCanFamPoodle1
+ subTrack chainNetPoodle off
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ color 100,50,0
+ altColor 255,240,200
+ matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+ matrixHeader A, C, G, T
+ type chain canFamPoodle1
+ otherDb canFamPoodle1
+
+ track netCanFamPoodle1
+ subTrack chainNetPoodle off
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign canFamPoodle1 chainCanFamPoodle1
+ otherDb canFamPoodle1