Mercurial > repos > yating-l > hubarchivecreator

changeset 58:a0fc8379223c draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 72268f816f10341dbe3f6b33f8d9170d859c9697
author yating-l
date Fri, 30 Jun 2017 15:44:17 -0400
parents b39dd0b5a166
children f311e21ef362
files Bed.py BedSimpleRepeats.py BedSpliceJunctions.py Gff3.py Gtf.py Psl.py templates/trackDb/layout.txt
diffstat 7 files changed, 14 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/Bed.py	Fri Jun 30 14:49:14 2017 -0400
+++ b/Bed.py	Fri Jun 30 15:44:17 2017 -0400
@@ -43,7 +43,9 @@
         with open(myBigBedFilePath, 'w') as self.bigBedFile:
             subtools.bedToBigBed(self.sortedBedFile.name,
                                  self.chromSizesFile.name,
-                                 self.bigBedFile.name)
+                                 self.bigBedFile.name,
+                                 extraIndex='name'
+                                 )
 
         # Create the Track Object
         self.createTrack(file_path=trackName,
--- a/BedSimpleRepeats.py	Fri Jun 30 14:49:14 2017 -0400
+++ b/BedSimpleRepeats.py	Fri Jun 30 15:44:17 2017 -0400
@@ -43,7 +43,8 @@
                                  self.chromSizesFile.name,
                                  bigBedFile.name,
                                  typeOption='bed4+12',
-                                 autoSql=auto_sql_option
+                                 autoSql=auto_sql_option,
+                                 extraIndex='name'
                                  )
 
         # Create the Track Object
--- a/BedSpliceJunctions.py	Fri Jun 30 14:49:14 2017 -0400
+++ b/BedSpliceJunctions.py	Fri Jun 30 15:44:17 2017 -0400
@@ -42,7 +42,8 @@
                                  self.chromSizesFile.name,
                                  bigBedFile.name,
                                  typeOption='bed12+1',
-                                 autoSql=auto_sql_option
+                                 autoSql=auto_sql_option,
+                                 extraIndex='name'
                                  )
 
         # Create the Track Object
--- a/Gff3.py	Fri Jun 30 14:49:14 2017 -0400
+++ b/Gff3.py	Fri Jun 30 15:44:17 2017 -0400
@@ -56,7 +56,8 @@
                                  bigBedFile.name,
                                  autoSql=auto_sql_option,
                                  typeOption='bed12+8',
-                                 tab=True)
+                                 tab=True,
+                                 extraIndex='name')
 
         # Create the Track Object
         self.createTrack(file_path=trackName,
--- a/Gtf.py	Fri Jun 30 14:49:14 2017 -0400
+++ b/Gtf.py	Fri Jun 30 15:44:17 2017 -0400
@@ -67,7 +67,8 @@
                                  bigBedFile.name,
                                  autoSql=auto_sql_option,
                                  typeOption='bed12+8',
-                                 tab=True)
+                                 tab=True,
+                                 extraIndex='name')
 
 
         # Create the Track Object
--- a/Psl.py	Fri Jun 30 14:49:14 2017 -0400
+++ b/Psl.py	Fri Jun 30 15:44:17 2017 -0400
@@ -49,7 +49,8 @@
                                  big_psl_file.name,
                                  autoSql=auto_sql_option,
                                  typeOption='bed12+12',
-                                 tab=True)
+                                 tab=True,
+                                 extraIndex='name')
 
         # Create the Track Object
         self.createTrack(file_path=trackName,
--- a/templates/trackDb/layout.txt	Fri Jun 30 14:49:14 2017 -0400
+++ b/templates/trackDb/layout.txt	Fri Jun 30 15:44:17 2017 -0400
@@ -70,6 +70,6 @@
 priority ${trackDb.priority}
 color ${trackDb.track_color}
 group ${trackDb.group_name.lower().replace(' ', '_')}
-
+searchIndex name
     % endif
 % endfor