diff trackObject.py @ 26:a4a54b925c73 draft

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

--- a/trackObject.py	Tue Mar 14 17:41:29 2017 -0400
+++ b/trackObject.py	Wed Mar 15 10:51:23 2017 -0400
@@ -5,6 +5,8 @@
 import utils
 import bedToGff3
 import blastxmlToGff3
+import tempfile
+import subprocess
 
 class trackObject:
     def __init__(self, chrom_size, genome, extra_files_path):
@@ -30,7 +32,14 @@
         '''
         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':
+                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:
@@ -45,10 +54,8 @@
             blastxmlToGff3.blastxml2gff3(dataFile, des_path)
         elif dataType == 'gtf':
             utils.gtfToGff3(dataFile, des_path, self.chrom_size)
-        track = {
-            'fileName': fileName,
-            'dataType': dataType
-        }
+        track['fileName'] = fileName
+        track['dataType'] = dataType
         self.tracks.append(track)