def cached_seq(self, padding_pos5, padding_pos3, strand='+'):
"""
Returns the cached sequence in the positive strand direction.
@param padding_pos5 The amount of padding (left) in the 5' end
on the positive strand
@param padding_pos3 The amount of padding (right) on the 3' end
on the positive strand
"""
# TODO unit test
if padding_pos5 > self.seq_padding_pos5:
padding_pos5 = self.seq_padding_pos5
if padding_pos3 > self.seq_padding_pos3:
padding_pos3 = self.seq_padding_pos3
start_idx = self.seq_padding_pos5 - padding_pos5
end_idx = -1*(self.seq_padding_pos3 - padding_pos3) or None # if 0, then None-- pass into idx
if self.negative_sequence:
seq = reverse_complement(self.negative_sequence)
else:
seq = self.positive_sequence
substr = seq[start_idx:end_idx]
if strand == '+':
return substr
else:
return reverse_complement(substr)
def manual(self):
c.assay_name = "Manual Entry"
seq = self.form_result['sequence']
c.amplicon_width = len(seq)
c.prefix_width = 0
c.suffix_width = 0
enzymes = self.__enzymes_from_form()
c.form = h.LiteralForm(
value = {'enzyme': ''},
option = {'enzyme': [('','--')]+[(e.cutseq, e.name) for e in enzymes]}
)
# TODO helper function for later (shared with sequence)
c.prefix_pct = 0
c.amplicon_pct = 100
c.suffix_pct = 0
c.amplicon_offset_pos = c.prefix_width
c.amplicon_offset_neg = c.suffix_width
c.positive_sequence = seq
c.negative_sequence = reverse_complement(seq)
c.found_sequence = True
c.left_padding = 0
c.right_padding = 0
c.assay_id = ''
c.enzymes = self.form_result['enzymes']
c.form = h.LiteralForm(
value = {'enzymes': ''},
option = {'enzymes': [('','--')]+[(e.cutseq, e.name) for e in enzymes]}
)
return render('/cutter/sequence.html')
def _observed_complement(cls, observed):
"""
Returns the reverse complement of observed bases, excluding deletions.
@param observed The observed column from the snp table row.
Assumes format '[-ACTG][/ACTG]*'
"""
return [reverse_complement(base) for base in cls._observed(observed)]
def __add_sequence_primer_display_attrs(self, seq, **kwargs):
assay = kwargs.get("assay", None)
if assay:
primer_fwd = assay.primer_fwd
primer_rev = assay.primer_rev
probe_seq = assay.probe_seq
else:
primer_fwd = kwargs.get("primer_fwd", None)
primer_rev = kwargs.get("primer_rev", None)
probe_seq = kwargs.get("probe_seq", None)
posq = seq.amplicon.positive_strand_sequence
negq = seq.amplicon.negative_strand_sequence
posf = posq.find(primer_fwd)
posn = posq.find(reverse_complement(primer_rev))
if posf != -1:
posq = "%s%s%s" % (posq[: len(primer_fwd)], posq[len(primer_fwd) : posn].lower(), posq[posn:])
negq = negq.lower()
else:
negf = negq.find(primer_fwd)
negn = negq.find(reverse_complement(primer_rev))
negq = "%s%s%s" % (negq[: len(primer_fwd)], negq[len(primer_fwd) : negn].lower(), negq[negn:])
posq = posq.lower()
if probe_seq:
posp = posq.upper().find(reverse_complement(probe_seq))
negp = negq.upper().find(reverse_complement(probe_seq))
if posp != -1:
# raise Exception, posq
posq = "%s|%s|%s" % (posq[:posp], posq[posp : posp + len(probe_seq)], posq[posp + len(probe_seq) :])
elif negp != -1:
negq = "%s|%s|%s" % (negq[:negp], negq[negp : negp + len(probe_seq)], negq[negp + len(probe_seq) :])
seq.positive_display_sequence = posq
seq.negative_display_sequence = negq[::-1]
return seq
def sequence_variant(self, sequence, mutation, strand="+"):
"""
Return the possible mutation(s) in the sequence due to
the sequence. For now, return the original sequence.
# TODO: probably not return the original sequence
"""
# first step: get positive string, standardizing so it's
# easier for me to think about
if sequence.strand == "-":
seq = sequence.reverse_complement()
else:
seq = sequence
if mutation["observed"] == "lengthTooLong":
# raise UnknownMutationError, "Could not read the variants for %s SNP %s at chr%s:%s-%s" % (mutation['class'], mutation['name'], mutation['chrom'], mutation['chromStart'], mutation['chromEnd'])
sequences = []
dup = self.__class__.duplicate(sequence)
dup2 = self.__class__.duplicate(sequence, name=mutation["name"])
xform = TransformedGenomeSequence.replace(
dup2,
mutation["chromStart"],
mutation["chromEnd"],
"?" * (mutation["chromEnd"] - mutation["chromStart"] + 1),
)
sequences.append(dup)
sequences.append(xform)
else:
klass = mutation["class"].lower().replace("-", "")
sequences = getattr(self.__class__, "_%s_sequence_variant" % klass, self.__class__._unknown_variant)(
seq, mutation
)
if strand == "-":
return [reverse_complement(s) for s in sequences]
else:
return sequences
