def main():
"""
Main flow control function for the script. Is sequential over the
following steps:
1. Parse arguments
2. Read in reference
3. Read in all query genomes in parallel
4. Write output matrices
5. Write stats files
"""
commandline_args = _parse_args()
if commandline_args.dto_file:
commandline_args = _parse_input_config(commandline_args)
logging.basicConfig(level=logging.WARNING)
from nasp.nasp_objects import ReferenceGenome, GenomeCollection
reference = ReferenceGenome()
import_reference(reference, commandline_args.reference_fasta,
commandline_args.reference_dups)
genomes = GenomeCollection()
genomes.set_reference(reference)
parse_input_files(commandline_args.input_files,
commandline_args.num_threads, genomes,
commandline_args.minimum_coverage,
commandline_args.minimum_proportion)
write_output_matrices(genomes, commandline_args.matrix_folder,
commandline_args.filter_matrix_format)
write_stats_data(genomes, commandline_args.stats_folder)
def setUp(self):
reference_path = testdata.REFERENCE_FASTA
dups_path = testdata.REFERENCE_DUPS
reference = ReferenceGenome()
reference.import_fasta_file(reference_path)
reference.import_dups_file(dups_path)
self.genome = GenomeCollection()
fasta = FastaGenome()
fasta.import_fasta_file(reference_path)
self.genome.add_genome(fasta)
self.genome.set_reference(reference)
# Statistics are gathered when the matrices are created
self.genome.write_to_matrices({})
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
def setUp(self):
reference_path = testdata.REFERENCE_FASTA
dups_path = testdata.REFERENCE_DUPS
reference = ReferenceGenome()
reference.import_fasta_file(reference_path)
reference.import_dups_file(dups_path)
self.genome = GenomeCollection()
fasta = FastaGenome()
fasta.import_fasta_file(reference_path)
self.genome.add_genome(fasta)
self.genome.set_reference(reference)
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
self.matrix_formats = [
{
'dataformat': 'matrix',
'handle': self.tmpfile,
'filter': ''
}
]
class GenomeCollectionBestSnpVcfTestCase(unittest.TestCase):
def setUp(self):
reference = ReferenceGenome()
with tempfile.NamedTemporaryFile(mode='w+') as tmpfile:
# Position 5 and 6 can be anything, the others must match the VCF REF column or an exception will be thrown.
tmpfile.write('>500WT1_test\nCCTGGGGA')
tmpfile.seek(0)
reference.import_fasta_file(tmpfile.name)
self.genome = GenomeCollection()
from nasp.vcf_to_matrix import read_vcf_file
for genome in read_vcf_file(reference, 10, .9, testdata.GATK_VCF):
self.genome.add_genome(genome)
self.genome.set_reference(reference)
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
self.matrix_formats = [
{
'dataformat': 'vcf',
'handle': self.tmpfile,
'filter': ''
}
]
def tearDown(self):
os.remove(self.tmpfile.name)
def test_send_to_matrix_handles(self):
expected = ''
self.genome.send_to_matrix_handles(self.matrix_formats)
with open(self.tmpfile.name) as handle:
self.assertEqual(expected, handle.readlines())
def setUp(self):
reference = ReferenceGenome()
with tempfile.NamedTemporaryFile(mode='w+') as tmpfile:
# Position 5 and 6 can be anything, the others must match the VCF REF column or an exception will be thrown.
tmpfile.write('>500WT1_test\nCCTGGGGA')
tmpfile.seek(0)
reference.import_fasta_file(tmpfile.name)
self.genome = GenomeCollection()
from nasp.vcf_to_matrix import read_vcf_file
for genome in read_vcf_file(reference, 10, .9, testdata.GATK_VCF):
self.genome.add_genome(genome)
self.genome.set_reference(reference)
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
self.matrix_formats = [
{
'dataformat': 'vcf',
'handle': self.tmpfile,
'filter': ''
}
]
def main():
"""
Main flow control function for the script. Is sequential over the
following steps:
1. Parse arguments
2. Read in reference
3. Read in all query genomes in parallel
4. Write output matrices
5. Write stats files
"""
commandline_args = _parse_args()
if commandline_args.dto_file:
commandline_args = _parse_input_config(commandline_args)
logging.basicConfig(level=logging.WARNING)
from nasp.nasp_objects import ReferenceGenome, GenomeCollection
reference = ReferenceGenome()
import_reference(reference, commandline_args.reference_fasta, commandline_args.reference_dups)
genomes = GenomeCollection()
genomes.set_reference(reference)
parse_input_files(commandline_args.input_files, commandline_args.num_threads, genomes,
commandline_args.minimum_coverage, commandline_args.minimum_proportion)
write_output_matrices(genomes, commandline_args.matrix_folder, commandline_args.filter_matrix_format)
write_stats_data(genomes, commandline_args.stats_folder)
class GenomeCollectionMasterMatrixFastaTestCase(unittest.TestCase):
def setUp(self):
reference_path = testdata.REFERENCE_FASTA
dups_path = testdata.REFERENCE_DUPS
reference = ReferenceGenome()
reference.import_fasta_file(reference_path)
reference.import_dups_file(dups_path)
self.genome = GenomeCollection()
fasta = FastaGenome()
fasta.import_fasta_file(reference_path)
self.genome.add_genome(fasta)
self.genome.set_reference(reference)
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
self.matrix_formats = [
{
'dataformat': 'matrix',
'handle': self.tmpfile,
'filter': ''
}
]
def tearDown(self):
os.remove(self.tmpfile.name)
def test_send_to_matrix_handles(self):
expected = """LocusID Reference None #SNPcall #Indelcall #Refcall #CallWasMade #PassedDepthFilter #PassedProportionFilter #A #C #G #T #Indel #NXdegen Contig Position InDupRegion SampleConsensus CallWasMade PassedDepthFilter PassedProportionFilter Pattern Pattern#
500WT1_test::1 A 0 0 1 1/1 1/1 1/1 1 0 0 0 0 0 500WT1_test 1 False True '11' 1
500WT1_test::2 G 0 0 1 1/1 1/1 1/1 0 0 1 0 0 0 500WT1_test 2 False True '11' 1
500WT1_test::3 C 0 0 1 1/1 1/1 1/1 0 1 0 0 0 0 500WT1_test 3 False True '11' 1
500WT1_test::4 G 0 0 1 1/1 1/1 1/1 0 0 1 0 0 0 500WT1_test 4 False True '11' 1
500WT1_test::5 C 0 0 1 1/1 1/1 1/1 0 1 0 0 0 0 500WT1_test 5 False True '11' 1
500WT1_test::6 C 0 0 1 1/1 1/1 1/1 0 1 0 0 0 0 500WT1_test 6 False True '11' 1
500WT1_test::7 C 0 0 1 1/1 1/1 1/1 0 1 0 0 0 0 500WT1_test 7 False True '11' 1
500WT1_test::8 A 0 0 1 1/1 1/1 1/1 1 0 0 0 0 0 500WT1_test 8 False True '11' 1
500WT1_test::9 A 0 0 1 1/1 1/1 1/1 1 0 0 0 0 0 500WT1_test 9 False True '11' 1
500WT1_test::10 T 0 0 1 1/1 1/1 1/1 0 0 0 1 0 0 500WT1_test 10 False True '11' 1"""
# ...
# There might be more data, but 10 samples is enough
self.genome.send_to_matrix_handles(self.matrix_formats)
with open(self.tmpfile.name) as handle:
for expect, observe in zip(expected.split('\n'), handle):
self.assertEqual(expect + '\n', observe)
class GenomeCollectionStatsTestCase(unittest.TestCase):
maxDiff = None
def setUp(self):
reference_path = testdata.REFERENCE_FASTA
dups_path = testdata.REFERENCE_DUPS
reference = ReferenceGenome()
reference.import_fasta_file(reference_path)
reference.import_dups_file(dups_path)
self.genome = GenomeCollection()
fasta = FastaGenome()
fasta.import_fasta_file(reference_path)
self.genome.add_genome(fasta)
self.genome.set_reference(reference)
# Statistics are gathered when the matrices are created
self.genome.write_to_matrices({})
self.tmpfile = tempfile.NamedTemporaryFile(mode='w', delete=False)
def tearDown(self):
os.remove(self.tmpfile.name)
def test_send_to_matrix_handles(self):
from vcf_to_matrix import write_stats_data
expected = (
"Contig reference_length reference_clean reference_clean (%) reference_duplicated reference_duplicated (%) all_called all_called (%) all_passed_coverage all_passed_coverage (%) all_passed_proportion all_passed_proportion (%) all_passed_consensus all_passed_consensus (%) quality_breadth quality_breadth (%) any_snps any_snps (%) best_snps best_snps (%) \n"
" stat descriptions go here\n"
"Whole Genome 3977 3977 100.00% 0 0.00% 3977 100.00% 3977 100.00% 3977 100.00% 3977 100.00% 3977 100.00% 0 0.00% 0 0.00% \n"
"500WT1_test 3977 3977 100.00% 0 0.00% 3977 100.00% 3977 100.00% 3977 100.00% 3977 100.00% 3977 100.00% 0 0.00% 0 0.00% \n"
)
with tempfile.TemporaryDirectory() as tmpdir:
write_stats_data(self.genome, tmpdir)
os.listdir(tmpdir)
with open(tmpdir + '/general_stats.tsv') as handle:
self.assertEqual(expected, ''.join(handle.readlines()))
