diff trackObject.py @ 12:e1f188b43750 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

--- a/trackObject.py	Tue Mar 14 14:00:30 2017 -0400
+++ b/trackObject.py	Tue Mar 14 14:31:36 2017 -0400
@@ -30,9 +30,7 @@
         '''
         fileName = os.path.basename(dataFile)
         des_path = os.path.join(self.raw_folder, fileName)
-        if dataType == 'gff3' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
-            if dataType == 'gff3':
-                self.checkGff3(dataFile)
+        if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
             try:
                 shutil.copyfile(dataFile, des_path)
             except shutil.Error as err1:
@@ -53,13 +51,16 @@
         }
         self.tracks.append(track)
 
-    def checkGff3(self, dataFile):
+
+
+'''
+    def checkGff3(self, dataFile, dataType):
         with open(dataFile, 'r') as f:
             for line in f:
                 if not line.startswith('#'):
                     seq_type = line.rstrip().split('\t')[2]
                     if seq_type == 'transcript':
-                        dataType = 'gff3-transcript'
-                        break
+                        return 'gff3-transcript'
                     if seq_type == 'mRNA':
-                        break
+                        return 'gff3'
+'''
\ No newline at end of file