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)