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