diff trackObject.py @ 0:e4f3f2ed4fa5 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trackObject.py	Fri Mar 10 13:48:19 2017 -0500
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+import os
+import shutil
+import utils
+import bedToGff3
+import blastxmlToGff3
+
+class trackObject:
+    def __init__(self, dataFile, dataType, chrom_size):
+        self.dataFile = dataFile
+        self.fileName = os.path.basename(dataFile)
+        self.dataType = dataType
+        self.chrom_size = chrom_size
+        try:
+            if not os.path.exists('raw'):
+                os.mkdir('raw')
+        except OSError as oserror:
+            print "Cannot create raw folder error({0}): {1}".format(oserror.errno, oserror.strerror)
+        else:
+            self.raw_folder = 'raw'
+
+    def addToRaw(self):
+        des_path = os.path.join(self.raw_folder, self.fileName)
+        if self.dataType == 'gff3' or self.dataType == 'fasta' or self.dataType == 'bam' or self.dataType == 'bigwig' or self.dataType == 'bai':
+            if self.dataType == 'gff3':
+                self.checkGff3()
+            try:
+                shutil.copyfile(self.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 self.dataType == 'bedSimpleRepeats':
+            bedToGff3.bedToGff3(self.dataFile, self.chrom_size, 'trfbig', des_path)
+        elif self.dataType == 'bedSpliceJunctions':
+            bedToGff3.bedToGff3(self.dataFile, self.chrom_size, 'regtools', des_path)
+        elif self.dataType == 'blastxml':
+            blastxmlToGff3.blastxml2gff3(self.dataFile, des_path)
+        elif self.dataType == 'gtf':
+            utils.gtfToGff3(self.dataFile, des_path, self.chrom_size)
+
+    def checkGff3(self):
+        with open(self.dataFile, 'r') as f:
+            for line in f:
+                if not line.startswith('#'):
+                    seq_type = line.rstrip().split('\t')[2]
+                    if seq_type == 'transcript':
+                        self.dataType = 'gff3-transcript'
+                        break
+                    if seq_type == 'mRNA':
+                        break