def LoadCSV2DB(filename):
db = MySQLDatabase(host='132.77.80.238',
user='******',
passwd='a1a1a1',
db='primero')
counter = 1
for row in csv.reader(open(filename, 'r')):
loc_id = int(row[1])
name = row[2]
seq = row[3]
seq = seq.replace(" ", "")
if name == "":
continue
box = int(floor(loc_id / 81)) + 1
residual = loc_id % 81
row = chr(int(floor(residual / 9)) + 65)
residual = residual % 9
col = residual + 1
db.Insert('primers_primer',
[counter, name, box, row, col, seq, '', loc_id])
counter += 1
db.Commit()
def main():
options = MakeOpts().parse_args()
VOL = options.vol
LABWARE = 'GRID40SITE3'
LIQ = options.liquid_class
# We should also state which directory where the evoware could find the worklist file
db = MySQLDatabase(host=options.host, user='******', port=3306,
passwd='a1a1a1', db='tecan')
plate_id = options.iteration % options.num_plates
exp_id, max_time = GetLastPlate(db, plate_id, options.reading_label)
data = GetMeasuredData(db, exp_id, max_time, plate_id, options.reading_label)
dilution_rows = GetDilutionRows(db, exp_id, plate_id, max_time, options.row_split)
print "dilution_rows:\n", dilution_rows
worklist = []
for split in xrange(dilution_rows.shape[0]):
for col in xrange(dilution_rows.shape[1]):
row = dilution_rows[split, col]
meas = data[row, col]
print col, row, meas
if (meas > options.threshold) and ( (row+1) % (8/options.row_split) != 0 ):
msg = "OD = %f --> dilute cell %s%d into cell %s%d" % (meas, chr(ord('A') + row), col+1, chr(ord('A') + row + 1), col+1)
print msg
worklist += [UserPrompt(msg)]
worklist += [Comm('A',LABWARE,row,col,VOL,LIQ)]
worklist += [Comm('D',LABWARE,row+1,col,VOL,LIQ)]
#labware,volume and liquid_class would be hard coded for now ...
worklist += [Tip()]
IncrementRow(db, exp_id, plate_id, col, row+1, max_time)
db.Commit()
if len(worklist) == 0:
sys.exit(0)
worklist = Header() + worklist + Footer()
f = open(options.worklist[0], 'w')
f.write('\n'.join(worklist))
f.close()
print "Done!"
sys.exit(1)
def main():
options = MakeOpts().parse_args()
path_dict = ReadPathCsv(options)
VOL = options.vol
MEDIA_VOL = 150 - VOL #volune of fresh media in designated well
LABWARE = 'GRID40SITE3'
EPNSTAND = 'EpnStand'
LIQ = options.liquid_class
# We should also state which directory where the evoware could find the worklist file
db = MySQLDatabase(host=options.host,
user='******',
port=3306,
passwd='a1a1a1',
db='tecan')
exp_id_dict, plate_id = read_exp_id_csv(options.exp_id_csv)
if options.plate not in exp_id_dict:
error(
'The measured plate (%d) does not have an exp_id in the CSV file' %
options.plate)
exp_id = exp_id_dict[options.plate]
max_time = GetLastPlate(db, exp_id, plate_id, options.reading_label)
data = GetMeasuredData(db, exp_id, max_time, plate_id,
options.reading_label)
path_step_dict = GetPathSteps(db, exp_id, plate_id, max_time, path_dict)
worklist = []
for path_label, path_step in path_step_dict.iteritems():
row, col = path_dict[path_label][path_step]
meas = data[row, col]
print path_label, path_step, col, row, meas
if (meas > options.threshold) and (path_step <
len(path_dict[path_label]) - 1):
next_row, next_col = path_dict[path_label][path_step + 1]
msg = "Current plate is : %d ) %s __ OD = %f --> dilute cell %s%d into cell %s%d" % (
options.plate, exp_id, meas, chr(ord('A') + row), col + 1,
chr(ord('A') + next_row), next_col + 1)
print msg
worklist += [UserPrompt(msg)]
worklist += [Comm('A', EPNSTAND, 0, 0, MEDIA_VOL, LIQ)]
worklist += [
Comm('D', LABWARE, next_row, next_col, MEDIA_VOL, LIQ)
]
worklist += [Comm('A', LABWARE, row, col, VOL, LIQ)]
worklist += [Comm('D', LABWARE, next_row, next_col, VOL, LIQ)]
#labware,volume and liquid_class would be hard coded for now ...
worklist += [Tip()]
IncrementRow(db, exp_id, plate_id, path_label, path_step + 1,
max_time, row, col, next_row, next_col)
db.Commit()
if len(worklist) == 0:
sys.exit(0)
worklist = Header() + worklist + Footer()
f = open(options.worklist[0], 'w')
f.write('\n'.join(worklist))
f.close()
print "Done!"
sys.exit(1)