Mercurial > repos > yating-l > jbrowse_hub

comparison trackObject.py @ 28:5580dbf2a31c draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty
author yating-l
date Wed, 15 Mar 2017 11:36:09 -0400
parents a4a54b925c73
children d8049deb0c97
comparison
equal deleted inserted replaced
27:e025fa070c8d 28:5580dbf2a31c
28 def addToRaw(self, dataFile, dataType): 28 def addToRaw(self, dataFile, dataType):
29 ''' 29 '''
30 Convert gff3, BED, blastxml and gtf files into gff3 files 30 Convert gff3, BED, blastxml and gtf files into gff3 files
31 and store converted files in folder 'raw' 31 and store converted files in folder 'raw'
32 ''' 32 '''
33
33 fileName = os.path.basename(dataFile) 34 fileName = os.path.basename(dataFile)
34 des_path = os.path.join(self.raw_folder, fileName) 35 des_path = os.path.join(self.raw_folder, fileName)
35 track = {} 36 track = {}
36 if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai': 37 if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
37 if dataType == 'bam': 38 if dataType == 'bam':
39 # JBrowse will raise error: not a BAM file if the filename hasn't .bam extension
40 fileName = os.path.basename(dataFile) + '.bam'
41 des_path = os.path.join(self.raw_folder, fileName)
38 bam_index = utils.createBamIndex(dataFile) 42 bam_index = utils.createBamIndex(dataFile)
39 indexname = os.path.basename(bam_index) 43 indexname = os.path.basename(bam_index)
40 des_path_for_index = os.path.join(self.raw_folder, indexname) 44 des_path_for_index = os.path.join(self.raw_folder, indexname)
41 shutil.copyfile(bam_index, des_path_for_index) 45 shutil.copyfile(bam_index, des_path_for_index)
42 track['index'] = indexname 46 track['index'] = indexname
47
43 try: 48 try:
44 shutil.copyfile(dataFile, des_path) 49 shutil.copyfile(dataFile, des_path)
45 except shutil.Error as err1: 50 except shutil.Error as err1:
46 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror) 51 print "Cannot move file, error({0}: {1})".format(err1.errno, err1.strerror)
47 except IOError as err2: 52 except IOError as err2: