def test_read_gf():
# Reads a default file
r = GenomicFeatures()
# we can also instanciate from another GenomicFeatures instance
r = GenomicFeatures(r)
# we can also instanciate from a valid dataframe
r = GenomicFeatures(r.df)
# test repr
r
# and print statement
print(r)
r.features
r.tissues
r.plot()
r.drop_tissue_in('breast')
r.drop_tissue_in(['skin', 'bone'])
r.keep_tissue_in(['cervix', 'lung'])
assert r.shift == 2
assert len(r.unique_tissues) == 2
gf1 = GenomicFeatures()
gf2 = GenomicFeatures(testing.genomic_features_csv)
to_drop = [x for x in gf1.df.index if x not in gf2.df.index]
gf1.drop_cosmic(to_drop)
gf1.features = gf2.features
assert gf2 == gf1
gf = GenomicFeatures(testing.genomic_features_bare_csv)
assert gf.shift == 1
gf.get_TCGA()
def test_read_gf():
# Reads a default file
r = GenomicFeatures()
# we can also instanciate from another GenomicFeatures instance
r = GenomicFeatures(r)
# we can also instanciate from a valid dataframe
r = GenomicFeatures(r.df)
# test repr
r
# and print statement
print(r)
r.features
r.tissues
r.plot()
r.drop_tissue_in('breast')
r.drop_tissue_in(['skin', 'bone'])
r.keep_tissue_in(['cervix', 'lung'])
assert r.shift == 2
assert len(r.unique_tissues) == 2
gf1 = GenomicFeatures()
gf2 = GenomicFeatures(testing.genomic_features_csv)
to_drop = [x for x in gf1.df.index if x not in gf2.df.index]
gf1.drop_cosmic(to_drop)
gf1.features = gf2.features
assert gf2 == gf1
gf = GenomicFeatures(testing.genomic_features_bare_csv)
assert gf.shift == 1
gf.get_TCGA()
def test_gf_compress():
gf = GenomicFeatures()
gf.compress_identical_features()
def test_gf_compress():
gf = GenomicFeatures()
gf.compress_identical_features()
