if len(argv) < 3:
print("usage: python makeoligo.py <fasta> <list>")
exit()
with open(argv[1], 'r') as f:
gene = f.readlines()[0].strip()
with open(argv[2], 'r') as l:
lis = [i.strip() for i in l.readlines() if i != '\n']
for line in lis:
seq = [gene[i:i + 3] for i in range(0, len(gene), 3)]
l = []
switches = re.split(r'\+', line)
for switch in switches:
old = switch[0]
i = int(''.join(switch[1:-1]))
new = switch[-1]
ori = aa_from_codon(seq[i - 1])
if old is ori:
seq[i - 1] = ecoli_codon[new].upper()
l += [i]
else:
e = 'error: you say ' + old + ' but seq has ' + ori
break
if l:
e = rc(''.join(seq[min(l) - 6:max(l) + 4]))
e = re.sub(r'([atcg]{15})[atcg]{0,}([atcg]{15})', r'\1,\2', e)
print '+'.join(switches) + ',' + e
codons = [cds[i : i + 3] for i in range(0, len(cds), 3)]
l = []
for switch in m:
old, i, new = switch
new1, old1 = (THREE_to_one(new), THREE_to_one(old))
ori = one_to_THREE(aa[codons[i]])
if old == ori:
codons[i] = ecoli_codon[new1].upper()
l += [i]
else:
print "error: mismatch when trying", old, i, new
if l:
e = rc("".join(codons[min(l) - 5 : max(l) + 6]))
e = re.sub(r"([atcg]{15})[atcg]{0,}([atcg]{15})", r"\1,\2", e)
handle = "+".join(["%s%s%s" % (THREE_to_one(s[0]), s[1], THREE_to_one(s[2])) for s in m])
orders += [{"name": handle, "oligos": [{"sequence": ee for ee in e.split(",")}]}]
# transcriptic output format
print json.dumps(
{
"parameters": {"ssDNA": "ssDNA/0", "mutants": orders},
"refs": {
"ssDNA": {
"aliquots": {"0": {"volume": "50:microliter"}},
"id": "<ssDNA to use>",
"store": "cold_20",
"type": "micro-1.5",
if len(argv) < 3:
print("usage: python makeoligo.py <fasta> <list>")
exit()
with open(argv[1], 'r') as f:
gene = f.readlines()[0].strip()
with open(argv[2], 'r') as l:
lis = [ i.strip() for i in l.readlines() if i != '\n' ]
for line in lis:
seq = [gene[i:i+3] for i in range(0, len(gene), 3)]
l = []
switches = re.split(r'\+', line)
for switch in switches:
old = switch[0]
i = int(''.join( switch[ 1:-1] ))
new = switch[-1]
ori = aa_from_codon( seq[i-1] )
if old is ori:
seq[i-1] = ecoli_codon[new].upper()
l += [i]
else :
e = 'error: you say ' + old + ' but seq has ' + ori
break
if l:
e = rc(''.join(seq[min(l)-6:max(l)+4]))
e = re.sub(r'([atcg]{15})[atcg]{0,}([atcg]{15})', r'\1,\2', e)
print '+'.join(switches) + ',' + e