def test_gff_sizes(self):
with tempfile.TemporaryDirectory() as tmpdirname:
gff_sizes = os.path.join(self.data_dir, 'sizes.gff3')
prepare_refseqs.format_sequences(gff_sizes=[gff_sizes],
out=tmpdirname)
def test_twobit(self):
with tempfile.TemporaryDirectory() as tmpdirname:
twobit = os.path.join(self.data_dir, 'a.2bit')
prepare_refseqs.format_sequences(twobit=twobit, out=tmpdirname)
def test_fastas(self):
with tempfile.TemporaryDirectory() as tmpdirname:
fastas = [
os.path.join(self.data_dir, fa) for fa in ('a.fa', 'b.fa')
]
prepare_refseqs.format_sequences(fastas=fastas, out=tmpdirname)
def test_indexed_fasta(self):
with tempfile.TemporaryDirectory() as tmpdirname:
fasta = os.path.join(self.data_dir, 'a.fa')
prepare_refseqs.format_sequences(indexed_fasta=fasta,
out=tmpdirname)
def test_gff(self):
with tempfile.TemporaryDirectory() as tmpdirname:
gff = os.path.join(self.data_dir, 'embed_fasta.gff3')
prepare_refseqs.format_sequences(gff=gff, out=tmpdirname)