def _update_genome_from_delta_data(franken_genome, external_genome,
parser_state, distance_covered,
is_external_insert):
from nasp.nasp_objects import Genome
if distance_covered == -1:
distance_covered = parser_state['final_pos'] - parser_state[
'reference_pos'] + 1
is_external_insert = True
if distance_covered > 0:
if parser_state['external_is_reversed']:
matching_segment = Genome.reverse_complement(''.join(
external_genome.get_call(
(parser_state['external_pos'] - distance_covered + 1),
parser_state['external_pos'])))
else:
matching_segment = ''.join(
external_genome.get_call(
parser_state['external_pos'],
(parser_state['external_pos'] + distance_covered - 1)))
franken_genome.set_call(matching_segment,
parser_state['reference_pos'], 'X')
parser_state[
'reference_pos'] = parser_state['reference_pos'] + distance_covered
parser_state['external_pos'] = parser_state['external_pos'] + (
-distance_covered
if parser_state['external_is_reversed'] else distance_covered)
if is_external_insert:
parser_state['external_pos'] += -1 if parser_state[
'external_is_reversed'] else 1
else:
franken_genome.set_call('.', parser_state['reference_pos'], '!')
parser_state['reference_pos'] += 1
return parser_state
def _update_genome_from_delta_data(franken_genome, external_genome, parser_state, distance_covered, is_external_insert):
from nasp.nasp_objects import Genome
if distance_covered == -1:
distance_covered = parser_state['final_pos'] - parser_state['reference_pos'] + 1
is_external_insert = True
if distance_covered > 0:
if parser_state['external_is_reversed']:
matching_segment = Genome.reverse_complement(''.join(
external_genome.get_call(( parser_state['external_pos'] - distance_covered + 1 ),
parser_state['external_pos'])))
else:
matching_segment = ''.join(external_genome.get_call(parser_state['external_pos'], (
parser_state['external_pos'] + distance_covered - 1 )))
franken_genome.set_call(matching_segment, parser_state['reference_pos'], 'X')
parser_state['reference_pos'] = parser_state['reference_pos'] + distance_covered
parser_state['external_pos'] = parser_state['external_pos'] + (
-distance_covered if parser_state['external_is_reversed'] else distance_covered )
if is_external_insert:
parser_state['external_pos'] += -1 if parser_state['external_is_reversed'] else 1
else:
franken_genome.set_call('.', parser_state['reference_pos'], '!')
parser_state['reference_pos'] += 1
return parser_state
class GenomeTestCase(unittest.TestCase):
def setUp(self):
self.genome = Genome()
@unittest.skip("Covered by GenomeStatus.set_value()")
def test_set_call(self):
pass
@unittest.skip("Covered by GenomeStatus.get_value()")
def test_get_call(self):
pass
# FIXME: it should throw an exception or the prefix should be optional
# If the prefix is missing, the contig will be appended to the previous contig
def test__import_fasta_line_missing_prefix(self):
expected = "SEQUENCE"
prefix = "prefix"
identifier = ">" + expected
self.genome._import_fasta_line(identifier, prefix)
self.assertListEqual([expected], self.genome.get_contigs())
# FIXME: assertRaises a specific Exception
def test__import_fasta_line_missing_identifier(self):
sequence = "ABCDGHMNRSTUVWXY"
with self.assertRaises(Exception):
self.genome._import_fasta_line(sequence)
# FIXME: assertRaises a specific Exception
def test__import_fasta_line_missing_contig(self):
with self.assertRaises(Exception):
self.genome._import_fasta_line("SEQUENCE1")
self.genome._import_fasta_line("SEQUENCE2")
def test__import_fasta_line_identifier_contains_spaces(self):
identifier = ">prefixName Description"
prefix = "prefix"
expected = "Name"
self.genome._import_fasta_line(identifier, prefix)
self.assertListEqual([expected], self.genome.get_contigs())
@unittest.skip("Covered by _import_fasta_file tests")
def test_import_fasta_file(self):
pass
def test_reverse_complement(self):
dna_string = "ABCDGHMNRSTUVWXYabcdghmnrstuvwxy"
expected = "rxwbaasynkdchgvtRXWBAASYNKDCHGVT"
dna_string2 = "ABCDGHKNRSTTVWXYabcdghknrsttvwxy"
self.assertEqual(expected, self.genome.reverse_complement(dna_string))
self.assertEqual(dna_string2, self.genome.reverse_complement(expected))
def test_simple_call(self):
expected = ["A", "C", "G", "T"]
for expect in expected:
self.assertEqual(expect, self.genome.simple_call(expect.lower()))
# It should check the base at position one
self.assertEqual("A", self.genome.simple_call("agctn"))
# It should replace uracil with thymine
self.assertEqual("T", self.genome.simple_call("u"))
# It should replace X with N if not allowed
self.assertEqual("N", self.genome.simple_call("X", allow_x=False))
self.assertEqual("X", self.genome.simple_call("X", allow_x=True))
# It should replace . with N if deletions are not allowed
self.assertEqual("N", self.genome.simple_call(".", allow_del=False))
self.assertEqual(".", self.genome.simple_call(".", allow_del=True))
# It should replace degeneracies with N
self.assertEqual("N", self.genome.simple_call("d"))
def test_simple_call_with_empty(self):
self.assertEqual("N", self.genome.simple_call("", allow_del=False))
self.assertEqual(".", self.genome.simple_call("", allow_del=True))
def test_simple_call_with_none(self):
self.assertEqual("N", self.genome.simple_call(None, allow_del=False))
self.assertEqual(".", self.genome.simple_call(None, allow_del=True))
class GenomeTestCase(unittest.TestCase):
def setUp(self):
self.genome = Genome()
@unittest.skip("Covered by GenomeStatus.set_value()")
def test_set_call(self):
pass
@unittest.skip("Covered by GenomeStatus.get_value()")
def test_get_call(self):
pass
# FIXME: it should throw an exception or the prefix should be optional
# If the prefix is missing, the contig will be appended to the previous contig
def test__import_fasta_line_missing_prefix(self):
expected = 'SEQUENCE'
prefix = 'prefix'
identifier = '>' + expected
self.genome._import_fasta_line(identifier, prefix)
self.assertListEqual([expected], self.genome.get_contigs())
# FIXME: assertRaises a specific Exception
def test__import_fasta_line_missing_identifier(self):
sequence = 'ABCDGHMNRSTUVWXY'
with self.assertRaises(Exception):
self.genome._import_fasta_line(sequence)
# FIXME: assertRaises a specific Exception
def test__import_fasta_line_missing_contig(self):
with self.assertRaises(Exception):
self.genome._import_fasta_line('SEQUENCE1')
self.genome._import_fasta_line('SEQUENCE2')
def test__import_fasta_line_identifier_contains_spaces(self):
identifier = '>prefixName Description'
prefix = 'prefix'
expected = 'Name'
self.genome._import_fasta_line(identifier, prefix)
self.assertListEqual([expected], self.genome.get_contigs())
@unittest.skip("Covered by _import_fasta_file tests")
def test_import_fasta_file(self):
pass
def test_reverse_complement(self):
dna_string = 'ABCDGHMNRSTUVWXYabcdghmnrstuvwxy'
expected = 'rxwbaasynkdchgvtRXWBAASYNKDCHGVT'
dna_string2 = 'ABCDGHKNRSTTVWXYabcdghknrsttvwxy'
self.assertEqual(expected, self.genome.reverse_complement(dna_string))
self.assertEqual(dna_string2, self.genome.reverse_complement(expected))
def test_simple_call(self):
expected = ['A', 'C', 'G', 'T']
for expect in expected:
self.assertEqual(expect, self.genome.simple_call(expect.lower()))
# It should check the base at position one
self.assertEqual('A', self.genome.simple_call('agctn'))
# It should replace uracil with thymine
self.assertEqual('T', self.genome.simple_call('u'))
# It should replace X with N if not allowed
self.assertEqual('N', self.genome.simple_call('X', allow_x=False))
self.assertEqual('X', self.genome.simple_call('X', allow_x=True))
# It should replace . with N if deletions are not allowed
self.assertEqual('N', self.genome.simple_call('.', allow_del=False))
self.assertEqual('.', self.genome.simple_call('.', allow_del=True))
# It should replace degeneracies with N
self.assertEqual('N', self.genome.simple_call('d'))
def test_simple_call_with_empty(self):
self.assertEqual('N', self.genome.simple_call('', allow_del=False))
self.assertEqual('.', self.genome.simple_call('', allow_del=True))
def test_simple_call_with_none(self):
self.assertEqual('N', self.genome.simple_call(None, allow_del=False))
self.assertEqual('.', self.genome.simple_call(None, allow_del=True))
