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)
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
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)
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)