--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trackObject.py	Wed Apr 12 17:41:55 2017 -0400
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+
+import os
+import shutil
+import utils
+import bedToGff3
+import blastxmlToGff3
+
+
+class trackObject:
+    def __init__(self, chrom_size, genome, extra_files_path):
+        self.chrom_size = chrom_size
+        outputDirect = os.path.join(extra_files_path, genome)
+        self.raw_folder = os.path.join(outputDirect, 'raw')
+        #Store metadata of the tracks
+        self.tracks = []
+        try:
+            if os.path.exists(self.raw_folder):
+                if os.path.isdir(self.raw_folder):
+                    shutil.rmtree(self.raw_folder)
+                else:
+                    os.remove(self.raw_folder)
+            os.makedirs(self.raw_folder)
+        except OSError as oserror:
+            print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
+
+    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 == 'bed' or dataType == 'gff3' or dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig':
+            if dataType == 'bam':
+                # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
+                extension = os.path.splitext(fileName)[1]
+                if extension != '.bam':
+                    fileName = fileName + '.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:
+                print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
+            except IOError as err2:
+                print "Cannot move file, error({0}: {1})".format(err2.errno, err2.strerror)
+        elif dataType == 'bedSimpleRepeats':
+            bedToGff3.bedToGff3(dataFile, self.chrom_size, 'trfbig', des_path)
+        elif dataType == 'bedSpliceJunctions':
+            bedToGff3.bedToGff3(dataFile, self.chrom_size, 'regtools', des_path)
+        elif dataType == 'blastxml':
+            blastxmlToGff3.blastxml2gff3(dataFile, des_path)
+        elif dataType == 'gtf':
+            utils.gtfToGff3(dataFile, des_path, self.chrom_size)
+        track['fileName'] = fileName
+        track['dataType'] = dataType
+        track['false_path'] = false_path
+        #self.SetMetadata(track, metaData)
+        self.tracks.append(track)
+
+    
\ No newline at end of file