diff trackObject.py @ 42:a5108e5010b4 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 149c5cbda82f49f260767b5710f0c2160eebc881-dirty

--- a/trackObject.py	Fri Mar 17 19:06:49 2017 -0400
+++ b/trackObject.py	Mon Mar 20 12:35:33 2017 -0400
@@ -24,19 +24,19 @@
         except OSError as oserror:
             print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
 
-    def addToRaw(self, dataFile, dataType, metaData):
+    def addToRaw(self, dataFile, dataType):
         """
         Convert gff3, BED, blastxml and gtf files into gff3 files 
         and store converted files in folder 'raw'
         """
-        
+        false_path = os.path.abspath(dataFile)
         fileName = os.path.basename(dataFile)
         des_path = os.path.join(self.raw_folder, fileName)
         track = {}
         if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
             if dataType == 'bam':
                 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
-                fileName = os.path.basename(dataFile) + '.bam'
+                fileName = fileName + '.bam'
                 des_path = os.path.join(self.raw_folder, fileName)
                 bam_index = utils.createBamIndex(dataFile)
                 indexname = os.path.basename(bam_index)
@@ -60,20 +60,8 @@
             utils.gtfToGff3(dataFile, des_path, self.chrom_size)
         track['fileName'] = fileName
         track['dataType'] = dataType
-        self.SetMetadata(track, metaData)
+        track['false_path'] = false_path
+        #self.SetMetadata(track, metaData)
         self.tracks.append(track)
 
-    #If the metadata is not set, use the default value
-    def SetMetadata(self, track, metaData):
-        track.update(metaData)
-        if 'name' not in metaData.keys() or track['name'] == '':
-            track['name'] = track['fileName']
-        if 'label' not in metaData.keys() or track['label'] == '':
-            track['label'] = track['name']
-        if 'track_color' not in metaData.keys() or track['track_color'] == '':
-            track['track_color'] = "#daa520"
-        if track['dataType'] == 'bigwig':
-            if 'pos_color' not in metaData.keys() or track['pos_color'] == '':
-                track['pos_color'] = "#FFA600"
-            if 'neg_color' not in metaData.keys() or track['neg_color'] == '':
-                track['neg_color'] = "#005EFF"
+    
\ No newline at end of file