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': ''
}
]
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': ''
}
]
