Ejemplo n.º 1
0
def _parseargs(argv):
    path = argv[1]
    outdir = argv[2] if len(argv) > 2 else None
    mode = argv[3].lower() if len(argv) > 3 else ''

    assay, _, _, _ = scrape_coords(path)

    d = dict()
    l = locals()
    params = ('path mode assay outdir')
    for p in params.split():
        d[p] = l[p]
    _setparams(d)
Ejemplo n.º 2
0
def _extract_wells_data(paths, wanted_features=None):
    nds = dict()
    for path in sorted(set(paths)):
        coords = scrape_coords(path)
        try:
            nds[coords] = _extract_field_data(path, wanted_features)
        except NoDataError:
            pass

    if not nds:
        raise NoDataError()

    return nds
Ejemplo n.º 3
0
def _parseargs(argv):
    path = argv[1]
    # e.g. scans/linkfarm/20100924_HCC1187/CK2/H12
    assay, plate, well, _ = scrape_coords(path)
#     row = well[0]
#     col = int(well[1:])
#     rownum = ord(row) - ord('A')
#     colnum = col - 1

    d = dict()
    l = locals()
    params = (# 'row col rownum colnum '
              'path assay plate well')
              
    for p in params.split():
        d[p] = l[p]
    _setparams(d)
Ejemplo n.º 4
0
def _parseargs(argv):
    nargs = len(argv)
    assert 2 < nargs < 5
    path = argv[1]

    assay, plate, well, _ = scrape_coords(path)
    extent = 'plate' if well is None else 'well'
    wavelength = argv[2]
    antibody = '%s_antibody' % wavelength

    d = dict()
    l = locals()
    params = ('path wavelength antibody '
              'assay plate well extent')

    for p in params.split():
        d[p] = l[p]
    _setparams(d)