def c_to_p(self, var_c, pro_ac=None):
"""
Converts a c. SequenceVariant to a p. SequenceVariant on the specified protein accession
Author: Rudy Rico
:param SequenceVariant var_c: hgvsc tag
:param str pro_ac: protein accession
:rtype: hgvs.sequencevariant.SequenceVariant
"""
if not (var_c.type == "c"):
raise HGVSInvalidVariantError("Expected a cDNA (c.) variant; got " + str(var_c))
if self._validator:
self._validator.validate(var_c)
reference_data = RefTranscriptData(self.hdp, var_c.ac, pro_ac)
builder = altseqbuilder.AltSeqBuilder(var_c, reference_data)
# TODO: handle case where you get 2+ alt sequences back;
# currently get list of 1 element loop structure implemented
# to handle this, but doesn't really do anything currently.
all_alt_data = builder.build_altseq()
var_ps = []
for alt_data in all_alt_data:
builder = altseq_to_hgvsp.AltSeqToHgvsp(reference_data, alt_data)
var_p = builder.build_hgvsp()
var_ps.append(var_p)
var_p = var_ps[0]
if self.add_gene_symbol:
self._update_gene_symbol(var_p, var_c.gene)
return var_p
def test_sequence_with_length_that_is_not_divisible_by_3(self):
hgvsc = "NM_999992.2:c.1del"
expected_sequence = "AAAATCAAATGGGGTAGGCCCGGCAGCCAGCTTTATAGAGGAGGCAGTTTCGCC"
with self.assertRaises(NotImplementedError):
ac_p = "DUMMY"
var = self._parser.parse_hgvs_variant(hgvsc)
transcript_data = RefTranscriptData(hdp=self._datasource, tx_ac=var.ac, pro_ac=ac_p)
def _run_comparison(self, hgvsc, expected_sequence):
ac_p = "DUMMY"
var = self._parser.parse_hgvs_variant(hgvsc)
transcript_data = RefTranscriptData(hdp=self._datasource, tx_ac=var.ac, pro_ac=ac_p)
builder = altseqbuilder.AltSeqBuilder(var, transcript_data)
insert_result = builder.build_altseq()
actual_sequence = insert_result[0].transcript_sequence
msg = "expected: {}\nactual : {}".format(expected_sequence, actual_sequence)
self.assertEqual(expected_sequence, actual_sequence, msg)