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()