comparison utils.py @ 26:a4a54b925c73 draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit e81fecac281f299db00cfc88a068e056b031ae9d-dirty

25:55c62db02917

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

26:a4a54b925c73

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

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')