diff TrackHub.py @ 31:d8049deb0c97 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty

--- a/TrackHub.py	Wed Mar 15 11:46:38 2017 -0400
+++ b/TrackHub.py	Fri Mar 17 12:28:32 2017 -0400
@@ -1,14 +1,10 @@
 #!/usr/bin/env python
 
 import os
-import trackObject
+import subprocess
+import shutil
 import utils
-import subprocess
-import string
-import shutil
-import tempfile
 
-#TODO: package JBrowse file conversion .pl files
 
 class TrackHub:
     def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path):
@@ -21,10 +17,6 @@
         self.raw = os.path.join(self.out_path, 'raw')
         self.json = os.path.join(self.out_path, 'json')
         try: 
-            if not self.out_path:
-                raise ValueError('empty output path\n')
-            if not os.path.exists(self.out_path):
-                raise ValueError('the output folder has not been created')
             if os.path.exists(self.json):
                 shutil.rmtree(self.json)
             os.makedirs(self.json)
@@ -39,7 +31,6 @@
             self.addTrack(input_file)
         self.indexName()
         self.makeArchive()
-        #shutil.rmtree(self.out_path)
         self.outHtml()
         print "Success!\n"
     
@@ -59,7 +50,7 @@
             bam_track = dict()
             bam_track['type'] = 'JBrowse/View/Track/Alignments2'
             bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
-            bam_track['label'] = track['fileName']
+            bam_track['label'] = track['label']
             bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
             bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
             utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')
@@ -68,14 +59,14 @@
             self.createTrackList()
             json_file = os.path.join(self.json, "trackList.json")
             bigwig_track = dict()
-            bigwig_track['label'] = track['fileName']
+            bigwig_track['label'] = track['label']
             bigwig_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
             bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
             bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
             utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')
         else: 
             gff3_file = os.path.join(self.raw, track['fileName'])
-            label = track['fileName']
+            label = track['label']
             if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf':
                 p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', 'CanvasFeatures', '--trackLabel', label, '--config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments"}', '--out', self.json])
             elif track['dataType'] == 'gff3_transcript':
@@ -98,7 +89,6 @@
     #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
     #run it locally. May need modify
     def outHtml(self):
-        #htmloutput = tempfile.NamedTemporaryFile(self.outfile, suffix = '.html', bufsize=0, delete=False)
         with open(self.outfile, 'w') as htmlfile:
             htmlstr = 'The JBrowse Hub is created: <br>'
             zipfiles = '<li><a href = "%s">Download</a></li>'
@@ -112,15 +102,13 @@
                         relative_file_path = os.path.join(relative_directory, file)
                         htmlstr += zipfiles % relative_file_path
                         
-            #htmlstr = htmlstr % zipfile
             htmlfile.write(htmlstr)
 
     def createTrackList(self):
         trackList = os.path.join(self.json, "trackList.json")
         if not os.path.exists(trackList):
             os.mknod(trackList)
-            #open(trackList,'w').close()
-            
+