comparison trackObject.py @ 12:e1f188b43750 draft

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

11:22efe9f6e8a8

        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)
        if dataType == 'gff3' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
            if dataType == 'gff3':
                self.checkGff3(dataFile)
            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:

            'fileName': fileName,
            'dataType': dataType
        }
        self.tracks.append(track)

    def checkGff3(self, dataFile):
        with open(dataFile, 'r') as f:
            for line in f:
                if not line.startswith('#'):
                    seq_type = line.rstrip().split('\t')[2]
                    if seq_type == 'transcript':
                        dataType = 'gff3-transcript'
                        break
                    if seq_type == 'mRNA':
                        break

12:e1f188b43750

        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)
        if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':
            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:

            'fileName': fileName,
            'dataType': dataType
        }
        self.tracks.append(track)



'''
    def checkGff3(self, dataFile, dataType):
        with open(dataFile, 'r') as f:
            for line in f:
                if not line.startswith('#'):
                    seq_type = line.rstrip().split('\t')[2]
                    if seq_type == 'transcript':
                        return 'gff3-transcript'
                    if seq_type == 'mRNA':
                        return 'gff3'
'''