def make_plasmid(repo, constituentparts, part, authorid, datecreated):
first = constituentparts[0]
last = constituentparts[len(constituentparts) - 1]
nsafirst = repository.get_annotations_by_family(repo, first['nucseq'], 'overhang')
nsalast = repository.get_annotations_by_family(repo, last['nucseq'], 'overhang')
if nsafirst[0]['startx'] < nsafirst[1]['startx']:
fpo = nsafirst[0]['feature']
else:
fpo = nsafirst[1]['feature']
if nsalast[0]['startx'] < nsalast[1]['startx']:
tpo = nsalast[0]['feature']
else:
tpo = nsalast[0]['feature']
allresistances = repository.get_features_by_family_name(repo, 'resistance')
resistancesforeachpart = get_resistance_by_composite_part(repo, constituentparts)
availresistances = find_satisfiable_resistance(0, resistancesforeachpart, allresistances)
if availresistances:
eligiblevectors = repository.find_vectors_by_overhang_resistance(repo, fpo, tpo, availresistances)
if eligiblevectors:
return repository.persist_plasmid(repo, 'PLASMID-' +
part['name'], part, eligiblevectors[0], authorid, datecreated)
return {}
def make_part(repo, p, concentration, concentration_unit, volume_unit):
part = {}
part['name'] = p['name'] + '-' + str(p['idpart'])
part['sequence'] = p['nucseq']['sequence'].upper()
part['concentration'] = concentration
part['concentrationUnit'] = concentration_unit
part['volumeUnit'] = volume_unit
nsa = repository.get_annotations_by_family(repo, p['nucseq'], 'overhang')
l = []
r = []
if nsa[0]['startx'] > nsa[1]['startx']:
l.append(nsa[1]['startx'])
l.append(nsa[1]['endx'])
r.append(nsa[0]['startx'])
r.append(nsa[0]['endx'])
else:
l.append(nsa[0]['startx'])
l.append(nsa[0]['endx'])
r.append(nsa[1]['startx'])
r.append(nsa[1]['endx'])
overhang = {}
overhang['fivePrimeEnd'] = l[0]
overhang['fivePrimeStart'] = l[1]
overhang['threePrimeEnd'] = r[0]
overhang['threePrimeStart'] = r[1]
part['overhangs'] = overhang
return part
def get_vector_overhang_annotations(repo, vectorname):
vector = [v for v in repo['vectors'] if v['name'].lower() == vectorname.lower()]
if len(vector) <= 0:
raise ValueError('There is an invalid vector (' + vectorname + ') in the plasmids file.')
vector = vector[0]
nucseqannotations = repository.get_annotations_by_family(repo, vector['nucseq'], 'overhang')
if len(nucseqannotations) != 2:
raise ValueError('Unexpected number of overhangs found in ' + vectorname + ' num is ', len(nucseqannotations))
return nucseqannotations
def get_resistance_by_composite_part(repo, constituentparts):
resistancesforeachpart = []
for pt in constituentparts:
possiblevectors = repository.get_vectors_by_part(repo, pt)
res = []
for vt in possiblevectors:
nsa = repository.get_annotations_by_family(repo, vt['nucseq'], 'resistance')
if len(nsa) > 1:
print('Warning: Multi resistance vector breaks assumption.')
if nsa:
res.append(nsa[0]['feature'])
resistancesforeachpart.append(res)
return resistancesforeachpart
def compute_part_sequence(repo, constituentparts):
sequence = ''
prev_endoverhang = ''
count = 0
for part in constituentparts:
if 'moclo' in part['format']['idformat'].lower():
# Get start and end overhangs for sequence
overhangs = repository.get_annotations_by_family(
repo, part['nucseq'], 'overhang')
startoverhang = overhangs[0]
endoverhang = overhangs[1]
if overhangs[0]['startx'] > overhangs[1]['startx']:
startoverhang = overhangs[1]
endoverhang = overhangs[0]
# Make sure the start overhang matches the previous sequence's end overhang
if prev_endoverhang and startoverhang['feature']['nucseq']['sequence'] != \
prev_endoverhang['feature']['nucseq']['sequence']:
raise ValueError(
"Consecutive composite parts don't have matching overhang values."
)
prev_endoverhang = endoverhang
if startoverhang['startx'] > 0:
raise ValueError(
'Part ' + part['name'] +
' does not begin with an overhang feature as expected '
'of a Modular Cloning part.')
end_overhang_len = len(
endoverhang['feature']['nucseq']['sequence'].strip())
# Add start overhang to sequence
sequence += startoverhang['feature']['nucseq']['sequence']\
.strip() + part['nucseq']['sequence'][:-end_overhang_len].strip()
count += 1
# Add end overhang to final sequence
sequence += endoverhang['feature']['nucseq']['sequence'].strip()
return sequence
