def new_pot(x, x_len, y, y_len):
mpotsnp = MeltingPotSNP(
a=''.join([before[before_len - shift:],
x,
after[:pr_len - shift - x_len]]),
am=''.join([before[before_len - shift:],
y,
after[:pr_len - shift - x_len]]),
b=reverse_complement(''.join(
[before[before_len - shift:],
x,
after[:pr_len - shift - y_len]])),
bm=reverse_complement(''.join(
[before[before_len - shift:],
y,
after[:pr_len - shift - y_len]])),
position=str(shift))
mpotsnp.meltDone.connect(self.on_melt_ready)
return mpotsnp
def task(self, task):
self.__task = task.replace(" ", "")
self.__task = task.replace("\n", "")
self.__melting_pots = []
patterns = {re.compile(SIMPLE_TASK_PATTERN, re.IGNORECASE):
TaskType.simple,
re.compile(SNP_TASK_PATTERN, re.IGNORECASE):
TaskType.snp,
re.compile(SNP_TASK_WITH_SHIFT_PATTERN, re.IGNORECASE):
TaskType.snp_shift,
re.compile(MISMATCH_TASK_PATTERN, re.IGNORECASE):
TaskType.mismatch,
re.compile(RANGE_TASK_PATTERN, re.IGNORECASE):
TaskType.cut_range,
}
self.__task_type = TaskType.error
match_result = None
for pat in patterns:
match_result = pat.match(self.__task)
if match_result:
self.__task_type = patterns[pat]
break
if self.__task_type is TaskType.simple:
self.__melting_pots = [MeltingPot(self.__task,
reverse_complement(self.__task))]
elif self.__task_type is TaskType.cut_range:
before = match_result.group('before')
variable = match_result.group('range')
after = match_result.group('after')
step = 1 if before else -1
variable_parts = [variable[:i]
for i in range(0, len(variable) + 1)] \
if before else \
reversed([variable[i:]
for i in range(0, len(variable) + 1)])
self.__melting_pots = [MeltingPot(
''.join([before, variable, after]),
reverse_complement(''.join([before, variable, after]))
)
for variable in variable_parts]
elif self.__task_type is TaskType.mismatch:
before = match_result.group('before')
a = match_result.group('a')
b = match_result.group('b')
after = match_result.group('after')
self.__melting_pots = [
MeltingPot(''.join([before, a, after]),
reverse_complement(''.join(
[before, b, after])))
]
elif self.__task_type is TaskType.snp:
before = match_result.group('before')
wt = match_result.group('wt')
mut = match_result.group('mut')
after = match_result.group('after')
self.__melting_pots = [
MeltingPot(''.join([before, wt, after]),
reverse_complement(''.join(
[before, wt, after]))),
MeltingPot(''.join([before, wt, after]),
reverse_complement(''.join(
[before, mut, after]))),
MeltingPot(''.join([before, mut, after]),
reverse_complement(''.join(
[before, mut, after]))),
MeltingPot(''.join([before, mut, after]),
reverse_complement(''.join(
[before, wt, after]))),
]
elif self.__task_type is TaskType.snp_shift:
before = match_result.group('before').lower()
before_len = len(before)
wt = match_result.group('wt').upper()
wt_len = len(wt)
mut = match_result.group('mut').upper()
mut_len = len(mut)
after = match_result.group('after').lower()
self.probeMin = int(match_result.group('min'))
self.probeMax = int(match_result.group('max'))
self.__task = '{bef}({wt}>{mut}){aft}'.format(bef=before,
wt=wt,
mut=mut,
aft=after,)
self.__melting_pots = []
for pr_len in range(self.probeMin, self.probeMax + 1):
for shift in range(0, pr_len):
def new_pot(x, x_len, y, y_len):
mpotsnp = MeltingPotSNP(
a=''.join([before[before_len - shift:],
x,
after[:pr_len - shift - x_len]]),
am=''.join([before[before_len - shift:],
y,
after[:pr_len - shift - x_len]]),
b=reverse_complement(''.join(
[before[before_len - shift:],
x,
after[:pr_len - shift - y_len]])),
bm=reverse_complement(''.join(
[before[before_len - shift:],
y,
after[:pr_len - shift - y_len]])),
position=str(shift))
mpotsnp.meltDone.connect(self.on_melt_ready)
return mpotsnp
self.melting_pots.append(
new_pot(wt, wt_len, mut, mut_len)
)
elif self.__task_type is TaskType.error:
raise MTaskParsingError
else:
raise MTaskParsingError
