def process_primer(self):
source = UCSCSequenceSource()
left_padding = 1000
right_padding = 1000
sequences = source.sequences_for_primers(
self.form_result["primer_fwd"], self.form_result["primer_rev"], left_padding, right_padding
)
# TODO: better selective update method
c.primer_fwd = self.form_result["primer_fwd"]
c.primer_rev = self.form_result["primer_rev"]
c.left_padding = left_padding
c.right_padding = right_padding
c.sequences = sequences
for seq in c.sequences:
seq.snps = self._get_snps(seq.chromosome, seq.start, seq.end)
self.__add_sequence_primer_display_attrs(
seq, primer_fwd=self.form_result["primer_fwd"], primer_rev=self.form_result["primer_rev"]
)
assayutil.set_amplicon_snps(c.sequences)
c.assay_form = h.LiteralForm(
value={"primer_fwd": self.form_result["primer_fwd"], "primer_rev": self.form_result["primer_rev"]}
)
return render("/assay/primer_output.html")
def process_location(self):
source = UCSCSequenceSource()
left_padding = 1000
right_padding = 1000
sequence = source.sequence_around_loc(
self.form_result["chromosome"],
self.form_result["location"],
self.form_result["width"],
left_padding,
right_padding,
)
# TODO: better selective update method
c.chromosome = self.form_result["chromosome"]
c.location = self.form_result["location"]
c.width = self.form_result["width"]
c.left_padding = left_padding
c.right_padding = right_padding
c.sequence = sequence
c.sequences = [sequence]
for seq in c.sequences:
seq.snps = self._get_snps(seq.chromosome, seq.start, seq.end)
seq.positive_display_sequence = seq.amplicon.positive_strand_sequence.lower()
seq.negative_display_sequence = seq.amplicon.negative_strand_sequence.lower()
assayutil.set_amplicon_snps(c.sequences)
c.assay_form = h.LiteralForm()
return render("/assay/location_output.html")
def process_snp(self):
snp_source = HG19Source()
seq_source = UCSCSequenceSource()
left_padding = 1000
right_padding = 1000
snps = snp_source.snps_by_rsid(self.form_result["snp_rsid"])
c.assay_form = h.LiteralForm()
c.snp_rsid = self.form_result["snp_rsid"]
c.width = self.form_result["width"]
# override
if not snps or len(snps) == 0:
# TODO: figure out how to make this appear on the field error instead
session["flash"] = "Could not find a SNP with the name %s" % self.form_result["snp_rsid"]
session["flash_class"] = "error"
session.save()
return render("/assay/snp_output.html")
sequences = []
for snp in snps:
chromStart = snp["chromStart"]
chromEnd = snp["chromEnd"]
# handle insertions and single variations, normally the chromStart
# refers to the gap just before the base #
if snp["chromStart"] == snp["chromEnd"]:
chromStart = chromEnd
else:
chromStart += 1
sequence = seq_source.sequence_around_region(
snp["chrom"][3:], chromStart, chromEnd, self.form_result["width"], left_padding, right_padding
)
# sequence.snps = self._get_snps(sequence.chromosome, sequence.start, sequence.end)
sequences.append(sequence)
c.left_padding = left_padding
c.right_padding = right_padding
c.sequences = sequences
for seq in c.sequences:
seq.snps = self._get_snps(seq.chromosome, seq.start, seq.end)
seq.positive_display_sequence = seq.amplicon.positive_strand_sequence.lower()
seq.negative_display_sequence = seq.amplicon.negative_strand_sequence.lower()[::-1]
assayutil.set_amplicon_snps(c.sequences)
return render("/assay/snp_output.html")
def view(self, id):
sequences = []
assay = Session.query(Assay).filter_by(id=id).first()
if not assay:
abort(404)
seq_source = UCSCSequenceSource()
snp_source = HG19Source()
sequences = assayutil.sequences_snps_for_assay(config, assay, seq_source, snp_source, 1000, 1000)
c.sequences = [tm_pcr_sequence(config, dg_pcr_sequence(config, seq)) for seq in sequences]
assayutil.set_amplicon_snps(c.sequences)
if assay.assay_type == Assay.TYPE_PRIMER:
for seq in c.sequences:
self.__add_sequence_primer_display_attrs(seq, assay=assay)
else:
for seq in c.sequences:
seq.positive_display_sequence = seq.amplicon.positive_strand_sequence.lower()
seq.negative_display_sequence = seq.amplicon.negative_strand_sequence.lower()[::-1]
c.assay = assay
c.hide_save = True
return render("/assay/view.html")
