def _write_domino_pools_file(designs, domino_pairs, name_well_pos,
filename, vol=1.0):
'''Writes domino pools operation file.'''
design_id_well_pos = {}
domino_file = open(filename + '_domino_pools.xls', 'w+')
domino_file.write(
'\t'.join(['DestinationPlateBarcode',
'DestinationPlateWell',
'SourcePlateBarcode',
'SourcePlateWell',
'ComponentName',
'Volume']) + '\n')
pos = 0
for design_id, design in designs.iteritems():
for domino in design['dominoes']:
well_pos = plate_utils.get_well_pos(pos)
seq = domino[1][0][0] + domino[1][1][0]
domino_id = _get_domino_id(seq, list(domino[0]), domino_pairs)
design_id_well_pos[design_id] = well_pos
line = '\t'.join([filename.split('/')[-1] + '_domino_pools',
well_pos,
filename.split('/')[-1],
name_well_pos[domino_id],
domino_id,
str(vol)])
domino_file.write(line + '\n')
pos += 1
domino_file.close()
return design_id_well_pos
def _write_parts_file(designs, filename):
'''Writes a parts list.'''
parts_well_pos = {}
parts_file = open(filename + '_parts.xls', 'w+')
parts_file.write(
'\t'.join(['Well', 'Part / plasmid id']) + '\n')
pos = 0
for design in designs.values():
for domino in design['dominoes']:
for part in domino[0]:
if part not in parts_well_pos:
well_pos = plate_utils.get_well_pos(pos)
parts_file.write('\t'.join([well_pos, part]) + '\n')
parts_well_pos[part] = well_pos
pos += 1
parts_file.close()
return parts_well_pos
def _write_dominoes_file(domino_pairs, filename):
'''Writes an order file.'''
order_file = open(filename + '.xls', 'w+')
order_file.write(
'\t'.join(['Well position', 'Name', 'Sequence', 'Notes']) + '\n')
name_well_pos = {}
pos = 0
for domino, pairs in domino_pairs.iteritems():
well_pos = plate_utils.get_well_pos(pos)
name = '_'.join(pairs[0])
name_well_pos[name] = well_pos
pairs_str = ', '.join(set([pair[0] + '_' + pair[1] for pair in pairs]))
order_file.write('\t'.join([well_pos, name, domino,
pairs_str]) + '\n')
pos += 1
order_file.close()
return name_well_pos
def _write_plasmids_file(designs, design_id_well_pos, part_well_pos,
filename, vol=1.0):
'''Writes plasmids file.'''
plasmids_file = open(filename + '_plasmids.xls', 'w+')
plasmids_file.write(
'\t'.join(['DestinationPlateBarcode',
'DestinationPlateWell',
'SourcePlateBarcode',
'SourcePlateWell',
'ComponentName',
'Volume']) + '\n')
pos = 0
for design_id, design in designs.iteritems():
well_pos = plate_utils.get_well_pos(pos)
parts = []
for domino in design['dominoes']:
for part in list(domino[0]):
if part not in parts:
line = '\t'.join([filename.split('/')[-1] + '_plasmids',
well_pos,
filename.split('/')[-1] + '_parts',
part_well_pos[part],
part,
str(vol)])
plasmids_file.write(line + '\n')
parts.append(part)
line = '\t'.join([filename.split('/')[-1] + '_plasmids',
well_pos,
filename.split('/')[-1] +
'_domino_pools',
design_id_well_pos[design_id],
design_id + '_domino_pool',
str(vol)])
plasmids_file.write(line + '\n')
pos += 1
plasmids_file.close()
