comparison utils.py @ 50:3e5b6f6a9abe draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty

49:193e94a43f0f

        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

def sequence_region(chrom_sizes):

    validChars = "_-%s%s" % (string.ascii_letters, string.digits)
    sanitized_name = ''.join([c if c in validChars else '_' for c in input_name])
    return "gonramp_" + sanitized_name

def createBamIndex(bamfile):
    p = subprocess.Popen(['samtools', 'index', bamfile])
    p.communicate()
    filename = bamfile + '.bai'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find bai file')

50:3e5b6f6a9abe

        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:
        subprocess.call(['faToTwoBit', reference, twoBitFile.name])
    except OSError as err:
        print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
    try:
        subprocess.call(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
    except OSError as err:
        print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
    return chrom_sizes

def sequence_region(chrom_sizes):

    validChars = "_-%s%s" % (string.ascii_letters, string.digits)
    sanitized_name = ''.join([c if c in validChars else '_' for c in input_name])
    return "gonramp_" + sanitized_name

def createBamIndex(bamfile):
    subprocess.call(['samtools', 'index', bamfile])
    filename = bamfile + '.bai'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find bai file')