Пример #1
0
def create_gmap_reference(reference_dir, reference_path, reference_name,
                          parameters=None):
    'It creates the reference fpath'

    cmd = ['gmap_build',  '-B',  get_external_bin_dir(), '-D',  reference_dir,
           '-d', reference_name]
    if parameters and 'kmer' in parameters:
        cmd.extend(['-k', str(parameters['kmer'])])
    cmd.append(reference_path)
    call(cmd,raise_on_error=True)

    fpath = '%s.coords' % reference_name
    if os.path.exists(fpath):
        os.remove(fpath)
Пример #2
0
def _modify_gmap_makefile(makefile):
    'It modifies the gmap makefile to use proper binaries'
    fhand = NamedTemporaryFile(delete=False)
    bin_dir = get_external_bin_dir()
    for line in open(makefile):
        if line.startswith('FA_COORDS'):
            line = 'FA_COORDS = %s/fa_coords\n' % bin_dir
        if line.startswith('MD_COORDS'):
            line = 'MD_COORDS = %s/md_coords\n' % bin_dir
        if line.startswith('GMAP_PROCESS'):
            line = 'GMAP_PROCESS = %s/gmap_process\n' % bin_dir
        if line.startswith('GMAPINDEX'):
            line = 'GMAPINDEX = %s/gmapindex\n' % bin_dir
        if line.startswith('PMAPINDEX'):
            line = 'PMAPINDEX = %s/pmapindex\n' % bin_dir
        fhand.write(line)
    fhand.flush()
    shutil.move(fhand.name, makefile)