comparison utils.py @ 5:e7c80e9b70ae draft

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

4:c7c1474a6b7d

        attr.append(s)
    gff3.write(';'.join(attr))
    gff3.write('\n')

def getChromSizes(reference, tool_dir):
    faToTwoBit = os.path.join(tool_dir, 'faToTwoBit')
    twoBitInfo = os.path.join(tool_dir, 'twoBitInfo')
    try:
        twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
        chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0, suffix='.chrom.sizes', delete=False)
    except IOError as err:
        print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
    try:
        p = subprocess.Popen([faToTwoBit, reference, twoBitFile.name])
        p.communicate()
    except OSError as err:
        print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
    try:
        p = subprocess.Popen([twoBitInfo, twoBitFile.name, chrom_sizes.name])
        p.communicate()
    except OSError as err:
        print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
    return chrom_sizes

                attribute['Parent'] = parents[gene_id]
                attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
                attribute['coverage'] = attr_li[3].split()[1].strip('"')
            write_features(field, attribute, gff3)
    gff3.close()

5:e7c80e9b70ae

        attr.append(s)
    gff3.write(';'.join(attr))
    gff3.write('\n')

def getChromSizes(reference, tool_dir):
    #TODO: find a better way instead of shipping the two exec files with the tool
    faToTwoBit = os.path.join(tool_dir, 'faToTwoBit')
    twoBitInfo = os.path.join(tool_dir, 'twoBitInfo')
    try:
        twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
        chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0, suffix='.chrom.sizes', delete=False)
    except IOError as err:
        print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
    try:
        p = subprocess.Popen(['faToTwoBit', reference, twoBitFile.name])
        p.communicate()
    except OSError as err:
        print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
    try:
        p = subprocess.Popen(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
        p.communicate()
    except OSError as err:
        print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
    return chrom_sizes

                attribute['Parent'] = parents[gene_id]
                attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
                attribute['coverage'] = attr_li[3].split()[1].strip('"')
            write_features(field, attribute, gff3)
    gff3.close()

def sanitize_name_path(input_path):
    '''
    Galaxy will name all the files and dirs as *.dat, 
    the function is simply replacing '.' to '_' for the dirs
    '''
    return input_path.replace('.', '_')