def test_write_fasta(create_testfolder, fasta_10x, filename, expected): out_fasta = str(create_testfolder) + "/" + filename + "_contig.fasta" fh = open(out_fasta, "w") fh.close() out = '' for l in fasta_10x: out = '>' + l + '\n' + fasta_10x[l] + '\n' ddl.utl.Write_output(out, out_fasta) assert len(list(create_testfolder.iterdir())) == expected
def test_write_fasta(create_testfolder, fasta_10x_mouse): out_fasta = str(create_testfolder) + "/filtered_contig.fasta" fh = open(out_fasta, "w") fh.close() out = '' for l in fasta_10x_mouse: out = '>' + l + '\n' + fasta_10x_mouse[l] + '\n' ddl.utl.Write_output(out, out_fasta) assert len(list(create_testfolder.iterdir())) == 1
def test_setup(create_testfolder, airr_reannotated, dummy_adata): vdj, adata = ddl.pp.filter_contigs(airr_reannotated, dummy_adata) assert airr_reannotated.shape[0] == 9 assert vdj.data.shape[0] == 7 assert vdj.metadata.shape[0] == 4 assert adata.n_obs == 5 f = create_testfolder / "test.h5" vdj.write_h5(f) assert len(list(create_testfolder.iterdir())) == 1 vdj2 = ddl.read_h5(f) assert vdj2.metadata is not None
def test_write_annotation(create_testfolder, annotation_10x, filename, expected): out_file = str( create_testfolder) + "/" + filename + "_contig_annotations.csv" annotation_10x.to_csv(out_file, index=False) assert len(list(create_testfolder.iterdir())) == expected
def test_write_annotation(create_testfolder, annotation_10x_mouse): out_file = str(create_testfolder) + "/filtered_contig_annotations.csv" annotation_10x_mouse.to_csv(out_file, index=False) assert len(list(create_testfolder.iterdir())) == 2
def test_write_annotation_tr2(create_testfolder, annotation_10x_tr2): out_file = str(create_testfolder) + "/all_contig_annotations.csv" annotation_10x_tr2.to_csv(out_file, index=False) assert len(list(create_testfolder.iterdir())) == 4
def test_write_airr(create_testfolder, airr_10x): out_file = str(create_testfolder) + "/test_airr_rearrangements.tsv" airr_10x.to_csv(out_file, sep='\t', index=False) assert len(list(create_testfolder.iterdir())) == 1