def read_vcf_file(reference, min_coverage, min_proportion, input_file):
"""
Submit VCF to be read in to VCF parser, populate genome data and filter
data from the parsed VCF data, return a list of the read-in genomes.
"""
genomes = {}
file_path = get_file_path(input_file)
with open(file_path, 'r') as vcf_filehandle:
from nasp.nasp_objects import VCFGenome, Genome, ReferenceCallMismatch, VCFRecord
vcf_record = VCFRecord(file_path)
vcf_samples = vcf_record.get_samples()
for vcf_sample in vcf_samples:
genomes[vcf_sample] = VCFGenome()
set_genome_metadata(genomes[vcf_sample], input_file)
genomes[vcf_sample].set_nickname(vcf_sample)
while vcf_record.fetch_next_record():
current_contig = vcf_record.get_contig()
current_pos = vcf_record.get_position()
# Skip if position isn't in reference; maybe user truncated reference to exclude an uninteresting region.
if current_pos <= reference.get_contig_length(current_contig):
reference_call = reference.get_call(current_pos, None, current_contig)
simplified_refcall = Genome.simple_call(reference_call)
if ( simplified_refcall != 'N' ) and (
simplified_refcall != Genome.simple_call(vcf_record.get_reference_call()[0]) ):
# Reference call from reference fasta differs from reference call in VCF file at the same position.
raise ReferenceCallMismatch(reference_call, vcf_record.get_reference_call(), file_path,
current_contig, current_pos)
for vcf_sample in vcf_samples:
sample_info = vcf_record.get_sample_info(vcf_sample)
# FIXME indels
if sample_info['call'] is not None:
genomes[vcf_sample].set_call(sample_info['call'], current_pos, 'X', current_contig)
if sample_info['was_called']:
genomes[vcf_sample].set_was_called('Y', current_pos, current_contig)
if sample_info['coverage'] is not None:
if sample_info['coverage'] == 'PASS' or sample_info['coverage'] >= min_coverage:
genomes[vcf_sample].set_coverage_pass('Y', current_pos, current_contig)
else:
genomes[vcf_sample].set_coverage_pass('N', current_pos, current_contig)
if sample_info['proportion'] is not None:
if sample_info['proportion'] == 'PASS' or sample_info['proportion'] >= min_proportion:
genomes[vcf_sample].set_proportion_pass('Y', current_pos, current_contig)
else:
genomes[vcf_sample].set_proportion_pass('N', current_pos, current_contig)
elif not sample_info['is_a_snp']:
# Some big SNP callers, like GATK, do not provide proportion information when
# the position is called reference. We cannot filter these positions.
genomes[vcf_sample].set_proportion_pass('-', current_pos, current_contig)
# from sys import stdout
#for genome in genomes:
# genomes[genome]._genome._send_to_fasta_handle( stdout )
return genomes.values()
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))
def read_vcf_file(reference, min_coverage, min_proportion, input_file):
"""
Submit VCF to be read in to VCF parser, populate genome data and filter
data from the parsed VCF data, return a list of the read-in genomes.
"""
genomes = {}
file_path = get_file_path(input_file)
with open(file_path, 'r') as vcf_filehandle:
from nasp.nasp_objects import VCFGenome, Genome, ReferenceCallMismatch, VCFRecord
vcf_record = VCFRecord(file_path)
vcf_samples = vcf_record.get_samples()
for vcf_sample in vcf_samples:
genomes[vcf_sample] = VCFGenome()
set_genome_metadata(genomes[vcf_sample], input_file)
genomes[vcf_sample].set_nickname(vcf_sample)
while vcf_record.fetch_next_record():
current_contig = vcf_record.get_contig()
current_pos = vcf_record.get_position()
# Skip if position isn't in reference; maybe user truncated reference to exclude an uninteresting region.
if current_pos <= reference.get_contig_length(current_contig):
reference_call = reference.get_call(current_pos, None,
current_contig)
simplified_refcall = Genome.simple_call(reference_call)
if (simplified_refcall !=
'N') and (simplified_refcall != Genome.simple_call(
vcf_record.get_reference_call()[0])):
# Reference call from reference fasta differs from reference call in VCF file at the same position.
raise ReferenceCallMismatch(
reference_call, vcf_record.get_reference_call(),
file_path, current_contig, current_pos)
for vcf_sample in vcf_samples:
sample_info = vcf_record.get_sample_info(vcf_sample)
# FIXME indels
if sample_info['call'] is not None:
genomes[vcf_sample].set_call(sample_info['call'],
current_pos, 'X',
current_contig)
if sample_info['was_called']:
genomes[vcf_sample].set_was_called(
'Y', current_pos, current_contig)
if sample_info['coverage'] is not None:
if sample_info['coverage'] == 'PASS' or sample_info[
'coverage'] >= min_coverage:
genomes[vcf_sample].set_coverage_pass(
'Y', current_pos, current_contig)
else:
genomes[vcf_sample].set_coverage_pass(
'N', current_pos, current_contig)
if sample_info['proportion'] is not None:
if sample_info['proportion'] == 'PASS' or sample_info[
'proportion'] >= min_proportion:
genomes[vcf_sample].set_proportion_pass(
'Y', current_pos, current_contig)
else:
genomes[vcf_sample].set_proportion_pass(
'N', current_pos, current_contig)
elif not sample_info['is_a_snp']:
# Some big SNP callers, like GATK, do not provide proportion information when
# the position is called reference. We cannot filter these positions.
genomes[vcf_sample].set_proportion_pass(
'-', current_pos, current_contig)
# from sys import stdout
#for genome in genomes:
# genomes[genome]._genome._send_to_fasta_handle( stdout )
return genomes.values()
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))
