comparison trackObject.py @ 31:d8049deb0c97 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit faeedda55e23f1197bc454d3db2d52af29d786e8-dirty

30:daf6a1122200

import os
import shutil
import utils
import bedToGff3
import blastxmlToGff3
import tempfile
import subprocess

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')
        print self.raw_folder
        self.tracks = []
        try:
            if os.path.exists(self.raw_folder):
                if os.path.isdir(self.raw_folder):
                    shutil.rmtree(self.raw_folder)

                    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'
        '''
        
        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':

            blastxmlToGff3.blastxml2gff3(dataFile, des_path)
        elif dataType == 'gtf':
            utils.gtfToGff3(dataFile, des_path, self.chrom_size)
        track['fileName'] = fileName
        track['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'
'''

31:d8049deb0c97

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)

                    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, metaData):
        """
        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)
        track = {}
        if dataType == 'gff3_mrna' or dataType == 'gff3_transcript' or dataType == 'fasta' or dataType == 'bam' or dataType == 'bigwig' or dataType == 'bai':

            blastxmlToGff3.blastxml2gff3(dataFile, des_path)
        elif dataType == 'gtf':
            utils.gtfToGff3(dataFile, des_path, self.chrom_size)
        track['fileName'] = fileName
        track['dataType'] = dataType
        track.update(metaData)
        if 'label' not in metaData.keys():
            track['label'] = fileName
        self.tracks.append(track)