def _get_exp_design(path,
_val=namedtuple('_val',
'ligand_name ligand_concentration time '
'antibody_0 antibody_1 coords'.split())):
# _key=namedtuple('_key', ('plate', 'well'))):
ret = NoClobberDict()
ks = []
ret = defaultdict(dict)
for record in read_exp_design(path):
plate = record.plate
row = record.row
column = record.column
well = '%s%02d' % (row.upper(), int(column))
# key = _key(plate, well)
ks.append((plate, well))
time = record.time__min_
ligand_name = record.ligand
ligand_concentration = record.concentration__ng_ml_
ab0 = parse_antibody_string(record.primary_body1)
ab1 = parse_antibody_string(record.primary_body2)
ret[plate][well] = _val(ligand_name, ligand_concentration,
time, ab0, ab1, plate + well)
assert len(ks) == len(set(ks))
return dict(ret)
def _get_exp_design(path,
_val=namedtuple(u'_val', u'treatment info'),
_treatment=namedtuple(u'_treatment',
u'ligand_name ligand_conc'
u'entration time antibodies'),
_antibody=namedtuple(u'_antibody',
u'target species wavelength'),
_info=namedtuple(u'_info',
u'replicate coords zone')):
# _key=namedtuple('_key', ('plate', 'well'))):
ks = []
replicate = defaultdict(int)
platemap = defaultdict(lambda: defaultdict(dict))
for record in read_exp_design(path):
plate = record.plate
try:
well = record.well.upper()
column = well[1:]
except AttributeError:
row = record.row
column = record.column
well = '%s%02d' % (row.upper(), int(column))
# key = _key(plate, well)
coords = (plate, well)
zone = (plate if plate.startswith('GF')
else plate + ('-L' if (int(column) - 1) < 6
else '-R'))
ks.append(coords)
time_ = record.time__min_
ligand_name = record.ligand
ligand_conc = record.concentration__ng_ml_
primary_abs = (parse_antibody_string(record.primary_body1),
parse_antibody_string(record.primary_body2))
secondary_abs = (parse_antibody_string(record.secondary_body1),
parse_antibody_string(record.secondary_body2))
abs_ = []
ws = set()
for primary, secondary in zip(primary_abs, secondary_abs):
ab_target, ab_species = primary
assert ab_species == secondary[0]
wavelength = secondary[2]
assert wavelength not in ws
ws.add(wavelength)
abs_.append((wavelength,
_antibody(*(primary + (wavelength,)))))
treatment = _treatment(ligand_name, ligand_conc, time_,
tuple(abs_))
repl = replicate[treatment]
replicate[treatment] += 1
info = _info(repl, coords, zone)
try:
assert repl == int(record.replicate)
except AttributeError:
pass
assert well not in platemap[plate]
platemap[plate][well] = _val(treatment, info)
assert len(ks) == len(set(ks))
return dict(platemap)
