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_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