def test_read10xvdj_cr6_folder(create_testfolder, json_10x_cr6, annotation_10x_cr6, fasta_10x_cr6):
fasta_file = str(create_testfolder) + "/test_filtered_contig.fasta"
json_file = str(create_testfolder) + "/test_all_contig_annotations.json"
annot_file = str(create_testfolder) + "/test_filtered_contig_annotations.csv"
annotation_10x_cr6.to_csv(annot_file, index=False)
vdj = ddl.read_10x_vdj(str(create_testfolder))
assert vdj.data.shape[0] == 26
assert vdj.data.shape[1] == 33
assert vdj.metadata.shape[0] == 10
assert vdj.metadata.shape[1] == 27
with open(json_file, 'w') as outfile:
json.dump(json_10x_cr6, outfile)
vdj = ddl.read_10x_vdj(str(create_testfolder))
assert vdj.data.shape[0] == 26
assert vdj.data.shape[1] == 49
assert vdj.metadata.shape[0] == 10
assert vdj.metadata.shape[1] == 27
assert not vdj.data.sequence.empty
os.remove(json_file)
fh = open(fasta_file, "w")
fh.close()
out = ''
for l in fasta_10x_cr6:
out = '>' + l + '\n' + fasta_10x_cr6[l] + '\n'
ddl.utl.Write_output(out, fasta_file)
vdj = ddl.read_10x_vdj(str(create_testfolder))
assert vdj.data.shape[0] == 26
assert vdj.data.shape[1] == 34
assert vdj.metadata.shape[0] == 10
assert vdj.metadata.shape[1] == 27
assert not vdj.data.sequence.empty
os.remove(fasta_file)
def test_to_scirpy(create_testfolder, annotation_10x, fasta_10x):
fasta_file = str(create_testfolder) + "/test_filtered_contig.fasta"
annot_file = str(create_testfolder) + "/test_filtered_contig_annotations.csv"
annotation_10x.to_csv(annot_file, index=False)
vdj = ddl.read_10x_vdj(str(create_testfolder))
assert vdj.data.shape[0] == 9
assert vdj.data.shape[1] == 20
assert vdj.metadata.shape[0] == 4
assert vdj.metadata.shape[1] == 25
adata = ddl.to_scirpy(vdj)
assert adata.obs.shape[0] == 5
assert adata.obs.shape[1] == 43
fh = open(fasta_file, "w")
fh.close()
out = ''
for l in fasta_10x:
out = '>' + l + '\n' + fasta_10x[l] + '\n'
ddl.utl.Write_output(out, fasta_file)
vdj = ddl.read_10x_vdj(str(create_testfolder))
assert vdj.data.shape[0] == 9
assert vdj.data.shape[1] == 21
assert vdj.metadata.shape[0] == 4
assert vdj.metadata.shape[1] == 25
assert not vdj.data.sequence.empty
adata = ddl.to_scirpy(vdj)
assert adata.obs.shape[0] == 5
assert adata.obs.shape[1] == 43
os.remove(fasta_file)
def test_filtercontigs(create_testfolder, dummy_adata_cr6, json_10x_cr6):
json_file = str(create_testfolder) + "/test_all_contig_annotations.json"
out_file = str(create_testfolder) + "/test_filtered.tsv"
with open(json_file, 'w') as outfile:
json.dump(json_10x_cr6, outfile)
vdj = ddl.read_10x_vdj(str(create_testfolder), filename_prefix='test_all')
vdj2, adata = ddl.pp.filter_contigs(vdj, dummy_adata_cr6)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 14
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj,
dummy_adata_cr6,
productive_only=False)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 23
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj,
dummy_adata_cr6,
productive_only=True,
simple=True)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 26
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj,
dummy_adata_cr6,
productive_only=False,
simple=True)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 26
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj,
dummy_adata_cr6,
productive_only=True,
filter_vj_chains=False)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 16
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj,
dummy_adata_cr6,
filter_vj_chains=False,
keep_highest_umi=False)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 17
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj, dummy_adata_cr6, filter_rna=True)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 14
assert adata.obs.shape[0] == 9
vdj2, adata = ddl.pp.filter_contigs(vdj,
dummy_adata_cr6,
productive_only=False,
filter_poorqualitycontig=True)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 23
assert adata.obs.shape[0] == 10
vdj2, adata = ddl.pp.filter_contigs(vdj, dummy_adata_cr6, save=out_file)
assert os.path.exists(out_file)
def test_read10xvdj_json(create_testfolder, json_10x_cr6):
json_file = str(create_testfolder) + "/test_all_contig_annotations.json"
with open(json_file, 'w') as outfile:
json.dump(json_10x_cr6, outfile)
vdj = ddl.read_10x_vdj(json_file)
assert vdj.data.shape[0] == 26
assert vdj.data.shape[1] == 49
assert vdj.metadata.shape[0] == 10
assert vdj.metadata.shape[1] == 27
os.remove(json_file)
def test_tofro_scirpy_cr6(create_testfolder, annotation_10x_cr6, json_10x_cr6):
json_file = str(create_testfolder) + "/test_all_contig_annotations.json"
annot_file = str(create_testfolder) + "/test_all_contig_annotations.csv"
annotation_10x_cr6.to_csv(annot_file, index=False)
with open(json_file, 'w') as outfile:
json.dump(json_10x_cr6, outfile)
vdj = ddl.read_10x_vdj(str(create_testfolder), filename_prefix = 'test_all')
assert vdj.data.shape[0] == 26
assert vdj.data.shape[1] == 33
assert vdj.metadata.shape[0] == 10
assert vdj.metadata.shape[1] == 27
adata = ddl.to_scirpy(vdj)
assert adata.obs.shape[0] == 10
assert adata.obs.shape[1] == 43
def test_setup2(create_testfolder, json_10x_cr6, dummy_adata_cr6):
json_file = str(create_testfolder) + "/test_all_contig_annotations.json"
with open(json_file, 'w') as outfile:
json.dump(json_10x_cr6, outfile)
vdj = ddl.read_10x_vdj(str(create_testfolder))
vdj, adata = ddl.pp.filter_contigs(vdj, dummy_adata_cr6)
assert vdj.data.shape[0] == 14
assert vdj.data.shape[1] == 50
assert vdj.metadata.shape[0] == 7
assert vdj.metadata.shape[1] == 25
ddl.tl.find_clones(vdj)
ddl.tl.generate_network(vdj, key='sequence')
ddl.tl.transfer(adata, vdj)
f = create_testfolder / "test.h5"
vdj.write_h5(f)
f2 = create_testfolder / "test.h5ad"
adata.write_h5ad(f2)
def test_filtercontigs_no_adata(create_testfolder):
json_file = str(create_testfolder) + "/test_all_contig_annotations.json"
vdj = ddl.read_10x_vdj(str(create_testfolder), filename_prefix='test_all')
vdj2 = ddl.pp.filter_contigs(vdj)
assert vdj.data.shape[0] == 26
assert vdj2.data.shape[0] == 14