def test_can_build_with_one_seq(self):
ref = ReferenceChromosome("TCATAAAAAAAT")
sequence_bank = SequenceBank(ref)
sequence_bank.add_sequence(".*G.........",
" ",
n_fwd=2,
n_rev=1)
builder = BAMBuilder(
os.path.join(self.work_dir,
self.filestub + ".bam")).with_bam_contig_data(
self.chrom, self.chrom_length, self.sample_name,
sequence_bank)
builder.build()
bam_file = pysam.Samfile(builder.filename, "rb")
reads = list(bam_file.fetch())
self.assertEqual(len(reads), 3)
for read in reads:
self.assertEqual(read.pos, 0)
self.assertEqual(read.seq, "TGTAAAAAAAT")
self.assertEqual(read.cigarstring, "1M1D10M")
self.assertTrue(os.path.isfile(bam_file.filename))
self.assertTrue(os.path.isfile(bam_file.filename.decode() + ".bai"))
def test_should_be_able_to_add_snp_using_whitespace_dsl_syntax(self):
# Given
input_ref = "CC*AAGG"
snp_input = " .T. "
# When
sequence_bank = SequenceBank(ReferenceChromosome(input_ref))
sequence_bank.add_sequence(snp_input)
read_lists = [builder.build_reads(0, {}) for builder in sequence_bank]
reads = [read for read_list in read_lists for read in read_list]
# Then
self.assertEqual(reads[0].pos, 2)
self.assertEqual(reads[0].seq, 'ATG')
def test_header_for_multisample_multicontig(self):
ref = ReferenceChromosome("")
sequence_bank = SequenceBank(ref)
builder = BAMBuilder(
os.path.join(self.work_dir, self.filestub + ".bam"))
builder.with_bam_contig_data("1", 10, "SAMPLE_ONE", sequence_bank)
builder.with_bam_contig_data("2", 20, "SAMPLE_TWO", sequence_bank)
expected_header = {
'HD': {
'VN': '1.0'
},
'SQ': [{
'LN': 10,
'SN': "1"
}, {
'LN': 20,
'SN': "2"
}],
'RG': [{
"ID": RG_ID + "_SAMPLE_ONE",
"SM": "SAMPLE_ONE"
}, {
"ID": RG_ID + "_SAMPLE_TWO",
"SM": "SAMPLE_TWO"
}]
}
self.assertDictEqual(expected_header, builder.header)
def test_should_fail_at_seq_with_different_length_to_reference(self):
# Given
ref_seq = "AAAA"
seq = "CC"
sequence_bank = SequenceBank(ReferenceChromosome(ref_seq))
# Then
self.assertRaises(weCallException, sequence_bank.add_sequence, seq)
def add_sample_name(self, sample_name):
if sample_name in self.__samples:
raise weCallException(
"Sample {} already exists in the SampleBank.".format(
sample_name))
sequence_bank = SequenceBank(self.reference)
self.__samples[sample_name] = sequence_bank
return sequence_bank
def test_should_use_sample_name_if_available(self):
chrom = '14'
sequence_bank = SequenceBank(
ReferenceChromosome('CGGCGGTCGAACGGAGCCCCAAGCGAAGCTCAAAACATGG', 0,
chrom))
sequence_bank.add_sequence(' ...........A............. ',
n_fwd=10,
n_rev=10)
driver = SVCDriver(self).with_ref_sequence(
'CGGCGGTCGAACGGAGCCCCAAGCGAAGCTCAAAACATGG', chrom=chrom)\
.with_bam_data('pi.bam', {'sample': sequence_bank}, True)
expect = driver.call()
expect.with_output_vcf().record_count(1).with_samples(['sample'])
def test_can_build_with_defined_quality(self):
ref = ReferenceChromosome("TCATAAAT")
sequence_bank = SequenceBank(ref)
sequence_bank.add_sequence(".*G.....", "9 87 00", n_fwd=1, n_rev=0)
builder = BAMBuilder(
os.path.join(self.work_dir,
self.filestub + ".bam")).with_bam_contig_data(
self.chrom, self.chrom_length, self.sample_name,
sequence_bank)
builder.build()
bam_file = pysam.Samfile(builder.filename, "rb")
reads = list(bam_file.fetch())
self.assertEqual(len(reads), 1)
self.assertEqual(reads[0].seq, "TGTAAAT")
# ascii: "0": "!", "1": "+", "2": "5", "3": "?", "4": "H", "5": "S",
# "6": "]", "7": "g", "8": "q", "9": "{"
expected_qual = "{qgHH!!"
self.assertEqual(reads[0].qual, expected_qual)
def setParallelAndSerialVariantCallers(self, copies1, copies2):
'''Prepare the variant caller data for the test to run'''
filestem = "vc_input"
ref_file_builder = FastaFileBuilder(os.path.join(self.work_dir, filestem + ".fa"))
ref1 = ref_file_builder.with_chrom(self.chrom1, self.ref_string1 * copies1)
ref2 = ref_file_builder.with_chrom(self.chrom2, self.ref_string2 * copies2)
self.repeat_length1 = ref1.length_minus_deletions() / copies1
self.repeat_length2 = ref2.length_minus_deletions() / copies2
ref_file_builder.build()
ref_file_builder.index()
seq_bank1 = SequenceBank(ref1)
seq_bank1.add_sequence(self.seq_string1 * copies1, n_fwd=10, n_rev=10)
seq_bank2 = SequenceBank(ref2)
seq_bank2.add_sequence(self.seq_string2 * copies2, n_fwd=10, n_rev=10)
seq_bank2.add_sequence(self.seq_string3 * copies2, n_fwd=10, n_rev=10)
bam_builder = BAMBuilder(os.path.join(self.work_dir, filestem + ".bam"))
bam_builder.with_bam_contig_data(ref1.chrom, ref1.length_minus_deletions(), self.sample_name1, seq_bank1)
bam_builder.with_bam_contig_data(ref2.chrom, ref2.length_minus_deletions(), self.sample_name2, seq_bank2)
bam_builder.build()
wecall_input_data = WecallInputData([bam_builder.filename], ref_file_builder.filename)
wecall_config_builder = WecallConfigBuilder(wecall_input_data, os.path.join(self.work_dir, filestem))
wecall_config_builder.with_configuration("maxBlockSize", self.block_size)
wecall_config_builder.with_configuration("noSimilarReadsFilter", False)
wecall_config_builder.with_configuration("maxClusterDist", 20)
wecall_config = wecall_config_builder.build()
parallel_output_file_stem = os.path.join(self.work_dir, filestem + "_parallel")
serial_output_file_stem = os.path.join(self.work_dir, filestem + "_serial")
self.vc_wrapper_parallel = VariantCallerWrapper(parallel_output_file_stem, wecall_config)
self.vc_wrapper_serial = VariantCallerWrapper(serial_output_file_stem, wecall_config)
def test_can_build_two_chroms(self):
ref1 = ReferenceChromosome("TCATAAAAAAAT")
sequence_bank1 = SequenceBank(ref1)
sequence_bank1.add_sequence(".*G.........")
ref2 = ReferenceChromosome("GGGG")
sequence_bank2 = SequenceBank(ref2)
sequence_bank2.add_sequence("..*.")
builder = BAMBuilder(
os.path.join(self.work_dir,
self.filestub + ".bam")).with_bam_contig_data(
"1", 100, "SAMPLE",
sequence_bank1).with_bam_contig_data(
"X", 50, "SAMPLE", sequence_bank2)
builder.build()
bam_file = pysam.Samfile(builder.filename, "rb")
reads_chrom1 = list(bam_file.fetch(region="1:1-20"))
self.assertEqual(len(reads_chrom1), 1)
self.assertEqual(reads_chrom1[0].seq, "TGTAAAAAAAT")
bam_file = pysam.Samfile(builder.filename, "rb")
reads_chrom2 = list(bam_file.fetch(region="X:1-5"))
self.assertEqual(len(reads_chrom2), 1)
self.assertEqual(reads_chrom2[0].seq, "GGG")
reads = list(bam_file.fetch())
self.assertEqual(len(reads), 2)
self.assertEqual(reads[0].seq, "TGTAAAAAAAT")
self.assertEqual(reads[1].seq, "GGG")
self.assertRaises(ValueError, bam_file.fetch, region="2:1-20")
self.assertTrue(os.path.isfile(bam_file.filename))
self.assertTrue(os.path.isfile(bam_file.filename.decode() + ".bai"))