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': ''
}
]
