Mercurial > repos > yating-l > jbrowsearchivecreator

diff trackObject.py @ 4:7e471cdd9e71 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973
author yating-l
date Fri, 07 Jul 2017 16:17:57 -0400
parents 804a93e87cc8
children
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line diff
--- a/trackObject.py	Wed May 31 15:45:47 2017 -0400
+++ b/trackObject.py	Fri Jul 07 16:17:57 2017 -0400
@@ -10,7 +10,7 @@
 class trackObject:
     def __init__(self, chrom_size, genome, extra_files_path):
         self.chrom_size = chrom_size
-        outputDirect = os.path.join(extra_files_path, genome)
+        outputDirect = os.path.join(extra_files_path, 'myHub')
         self.raw_folder = os.path.join(outputDirect, 'raw')
         #Store metadata of the tracks
         self.tracks = []
@@ -56,6 +56,8 @@
             bedToGff3.bedToGff3(dataFile, self.chrom_size, 'trfbig', des_path)
         elif dataType == 'bedSpliceJunctions':
             bedToGff3.bedToGff3(dataFile, self.chrom_size, 'regtools', des_path)
+        elif dataType == 'bigpsl':
+            bedToGff3.bedToGff3(dataFile, self.chrom_size, 'blat', des_path)
         elif dataType == 'blastxml':
             blastxmlToGff3.blastxml2gff3(dataFile, des_path)
         elif dataType == 'gtf':