diff trackObject.py @ 28:5580dbf2a31c draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

--- a/trackObject.py	Wed Mar 15 10:54:24 2017 -0400
+++ b/trackObject.py	Wed Mar 15 11:36:09 2017 -0400
@@ -30,16 +30,21 @@
         Convert gff3, BED, blastxml and gtf files into gff3 files 
         and store converted files in folder 'raw'
         '''
+        
         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'
+                des_path = os.path.join(self.raw_folder, fileName)
                 bam_index = utils.createBamIndex(dataFile)
                 indexname = os.path.basename(bam_index)
                 des_path_for_index = os.path.join(self.raw_folder, indexname)
                 shutil.copyfile(bam_index, des_path_for_index)  
                 track['index'] = indexname
+
             try:
                 shutil.copyfile(dataFile, des_path)
             except shutil.Error as err1: