def get_strands_tube_three(self):
tubes = []
count = 1 # 记录试管数目
for i in range(self.len_gene):
for j in range(i, self.len_gene):
for k in range(j, self.len_gene):
strands = {
Strand(self.gene_list[i],
name="t{0}:L{1}".format(count, i)):
self.c_gene,
Strand(self.gene_list[j],
name="t{0}:M{1}".format(count, j)):
self.c_gene,
Strand(self.gene_list[k],
name="t{0}:R{1}".format(count, k)):
self.c_gene
}
tubes.append(
Tube(
strands=strands,
complexes=SetSpec(max_size=3), # max_size,使用变量代替？
name='t{0}'.format(
count))) # complexes defaults to [A, B]
count += 1
return tubes
def analysis_all(self):
count = self.len_g1 + self.len_g2
strands = self.get_strands()
my_model = Model(material='dna', celsius=self.temp)
t1 = Tube(strands=strands,
complexes=SetSpec(max_size=count),
name='t1') # complexes defaults to [A, B]
tube_results = tube_analysis(tubes=[t1], model=my_model)
def get_strand_tube_all(self):
# 获取试管中只有两条基因片段的所有情况
strands = {}
for i in range(1, len(self.oligo) - 1):
strands[Strand(self.oligo[i][1],
name=self.oligo[i][0])] = self.oligo_conc
strands[Strand(self.oligo[0][1],
name=self.oligo[0][0])] = self.primer_conc
strands[Strand(self.oligo[-1][1],
name=self.oligo[-1][0])] = self.primer_conc
my_model = Model(material='dna', celsius=self.temp)
t = Tube(strands=strands, complexes=SetSpec(max_size=2),
name='t') # complexes defaults to [A, B]
tube_results = tube_analysis(tubes=[t], model=my_model)
all_conc = {}
for my_complex, conc in tube_results.tubes[
t].complex_concentrations.items():
all_conc[my_complex.name] = conc # 反应后每个试管中DNA的浓度
all_conc = sorted(all_conc.items(), key=lambda d: d[1],
reverse=True) # 排序
error = {}
for key, val in all_conc:
if key.count('+') == 1 and val > self.first_check:
tem_split = key[1:-1].split('+') # # 先去除括号，在根据+分割字符串
t1 = tem_split[0][1:]
t2 = tem_split[1][1:]
# print(t1, t2)
# print(t1.isdigit(), t2.isdigit())
if not t1.isdigit() or not t2.isdigit():
# 处理含有primer的片段，都是错配的
# primer+pirmer, primer+x , x+primer
error['{0}, {1}'.format(tem_split[0], tem_split[1])] = val
elif tem_split[0][0] == tem_split[1][0]: # 错配
# Rx+Rx ; Fx+Fx
error['{0}, {1}'.format(tem_split[0], tem_split[1])] = val
elif tem_split[0][0] == 'F' and int(t1) - int(t2) not in [
0, 1
]:
error['{0}, {1}'.format(tem_split[0], tem_split[1])] = val
elif tem_split[0][0] == 'R' and int(t1) - int(t2) not in [
0, -1
]:
error['{0}, {1}'.format(tem_split[0], tem_split[1])] = val
# 判断条件有待改进
elif val < self.first_check: #
break
print(error)
return error
def verification_two(self, list1):
# 验证错配的是否有问题
set1 = set()
strands = {}
for i in range(len(list1)):
for j in range(len(list1[i])):
if j == 0:
set1.add(list1[i][j])
strands[Strand(
self.gene_list[list1[i][j] - 1],
name="E:{1}:{0}".format(list1[i][j],
i))] = self.c_gene * 2 # 改正浓度
elif Strand(self.gene_list[list1[i][j] - 1],
name=str(list1[i][j])) in strands.keys():
strands[Strand(self.gene_list[list1[i][j] - 1],
name=str(list1[i][j]))] = self.c_gene * 2
else:
strands[Strand(self.gene_list[list1[i][j] - 1],
name=str(list1[i][j]))] = self.c_gene
tube = Tube(strands=strands,
complexes=SetSpec(max_size=len(list1)),
name="test")
my_model = Model(material='dna', celsius=self.temp)
tube_results = tube_analysis(tubes=[tube], model=my_model)
all_conc = {}
# print(tube_results)
# print("____________-")
for my_complex, conc in tube_results.tubes[
tube].complex_concentrations.items():
all_conc[my_complex.name] = conc
name = my_complex.name[1:-1]
# if name.count("E") == 2: #
if name.count("E") == len(list1) and conc > self.second_check: #
name_list = name.split("+")
set_t = set()
for i in range(len(list1)):
set_t.add(name_list[i][2])
if len(set_t) == len(list1) and set_t == set1: # 只关注错配的那几条
# print(name, conc)
return False
# print(name, conc)
new_conc = sorted(all_conc.items(), key=lambda d: d[1], reverse=True)
def get_strands_tube_tow(self):
# 获取试管中只有两条基因片段的所有情况
tubes = []
count = 1
for i in range(self.len_gene):
for j in range(i, self.len_gene):
strands = {
Strand(self.gene_list[i],
name="t{0}:L{1}".format(count, i)):
self.c_gene,
Strand(self.gene_list[j],
name="t{0}:R{1}".format(count, j)):
self.c_gene
}
tubes.append(
Tube(strands=strands,
complexes=SetSpec(max_size=2),
name='t{0}'.format(count)))
count += 1
return tubes