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 = 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 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': ''
}
]