def test_build_url_mouse(self):
downloader = fasta.Downloader()
url, release = downloader.build_url('all', 'mouse', None)
exp_release = self._expected_current_release('mouse')
expected = ('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_'
f'mouse/release_{exp_release}/gencode.v{exp_release}.transcripts.fa.gz')
assert url == expected
def test_build_url(self):
downloader = fasta.Downloader()
url, release = downloader.build_url('lncRNA', 'human', None)
exp_release = self._expected_current_release('human')
expected = ('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_'
f'human/release_{exp_release}/gencode.v{exp_release}.lncRNA_transcripts.fa.gz')
assert url == expected
def test_build_url_mouse(self):
downloader = fasta.Downloader()
url, release = downloader.build_url("all", "mouse", None)
exp_release = self._expected_current_release("mouse")
expected = (
"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_"
f"mouse/release_{exp_release}/gencode.v{exp_release}.transcripts.fa.gz"
)
assert url == expected
def test_build_url(self):
downloader = fasta.Downloader()
url, release = downloader.build_url("lncRNA", "human", None)
exp_release = self._expected_current_release("human")
expected = (
"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_"
f"human/release_{exp_release}/gencode.v{exp_release}.lncRNA_transcripts.fa.gz"
)
assert url == expected
def test_gunzip(self, tmpdir):
test_path = Path(tmpdir, 'test.txt.gz')
unzipped = Path(tmpdir, 'test.txt')
content = 'Hello, World!'.encode()
with gzip.open(test_path, 'wb') as test_file:
test_file.write(content)
fasta.Downloader().gunzip(str(test_path))
assert not test_path.exists()
assert unzipped.exists()
assert unzipped.read_text() == content.decode()
def test_build_url_pc22(self):
downloader = fasta.Downloader()
url, release = downloader.build_url('pc', 'human', '22')
expected = ('ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_'
'human/release_22/gencode.v22.pc_transcripts.fa.gz')
assert url == expected
def test_find_current_release(self):
release = fasta.Downloader().find_current_release('human')
expected = self._expected_current_release('human')
assert expected == release
def test_build_url_pc22(self):
downloader = fasta.Downloader()
url, release = downloader.build_url("pc", "human", "22")
expected = ("ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_"
"human/release_22/gencode.v22.pc_transcripts.fa.gz")
assert url == expected
def _run_download_gencode(biotype, species, release, out_path, unzip):
# Note: This function is separated for testing purposes.
downloader = fasta.Downloader()
downloader.get_gencode(biotype, species, release, out_path, unzip)
