def test_ucsc_gencode_gtf():
with TemporaryDirectory() as tmpdir:
gtf = GTF(UCSC_GENCODE_PATH, cache_directory_path=tmpdir)
df = gtf.dataframe(save_to_disk=False)
exons = df[df["feature"] == "exon"]
# expect 12 exons from the dataframe
assert len(exons) == 12, "Expected 12 exons, got %d: %s" % (len(exons), exons)
df2 = gtf.dataframe(save_to_disk=True)
assert len(df) == len(df2), "Got different length DataFrame"
assert list(df.columns) == list(df2.columns)
def test_ucsc_gencode_gtf():
with TemporaryDirectory() as tmpdir:
gtf = GTF(UCSC_GENCODE_PATH, cache_directory_path=tmpdir)
df = gtf.dataframe(save_to_disk=False)
exons = df[df["feature"] == "exon"]
# expect 12 exons from the dataframe
assert len(exons) == 12, \
"Expected 12 exons, got %d: %s" % (len(exons), exons)
df2 = gtf.dataframe(save_to_disk=True)
assert len(df) == len(df2), "Got different length DataFrame"
assert list(df.columns) == list(df2.columns)
def test_ucsc_refseq_gtf():
"""
Test GTF object with a small RefSeq GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
with TemporaryDirectory() as tmpdir:
gtf = GTF(UCSC_REFSEQ_PATH, cache_directory_path=tmpdir)
df = gtf.dataframe(save_to_disk=False)
exons = df[df["feature"] == "exon"]
# expect 16 exons from the GTF
assert len(exons) == 16, "Expected 16 exons, got %d: %s" % (len(exons), exons)
df2 = gtf.dataframe(save_to_disk=True)
assert len(df) == len(df2), "Got different length DataFrame"
assert list(df.columns) == list(df2.columns)
def test_ucsc_refseq_gtf():
"""
Test GTF object with a small RefSeq GTF file downloaded from
http://genome.ucsc.edu/cgi-bin/hgTables
"""
with TemporaryDirectory() as tmpdir:
gtf = GTF(UCSC_REFSEQ_PATH, cache_directory_path=tmpdir)
df = gtf.dataframe(save_to_disk=False)
exons = df[df["feature"] == "exon"]
# expect 16 exons from the GTF
assert len(exons) == 16, \
"Expected 16 exons, got %d: %s" % (
len(exons), exons)
df2 = gtf.dataframe(save_to_disk=True)
assert len(df) == len(df2), "Got different length DataFrame"
assert list(df.columns) == list(df2.columns)
def test_gtf_creates_csv_files_in_cache_dir():
"""
Make sure that GTF obeys the cache_dir argument by creating all of its
index files there.
"""
with TemporaryDirectory() as tmpdir:
gtf_object = GTF(gtf_path, cache_directory_path=tmpdir)
csv_path = gtf_object.data_subset_path()
assert tmpdir in csv_path, \
"Expected CSV path %s to contain cache_dir" % csv_path
search_pattern = join(tmpdir, "*mouse*")
assert len(glob(search_pattern)) == 0, \
"Temporary directory should be empty"
# creating the dataframe should have the effect of triggering
# GTF parsing and then saving the parsed results in a csv file
gtf_object.dataframe()
assert len(glob(search_pattern)) > 0, \
"Expected GTF to save files in cache_dir"
def test_gtf_creates_csv_files_in_cache_dir():
"""
Make sure that GTF obeys the cache_dir argument by creating all of its
index files there.
"""
with TemporaryDirectory() as tmpdir:
gtf_object = GTF(gtf_path, cache_directory_path=tmpdir)
csv_path = gtf_object.data_subset_path()
assert tmpdir in csv_path, \
"Expected CSV path %s to contain cache_dir" % csv_path
search_pattern = join(tmpdir, "*mouse*")
assert len(glob(search_pattern)) == 0, \
"Temporary directory should be empty"
# creating the dataframe should have the effect of triggering
# GTF parsing and then saving the parsed results in a csv file
gtf_object.dataframe()
assert len(glob(search_pattern)) > 0, \
"Expected GTF to save files in cache_dir"
