def test_download_genome():
genome.main(["genome", "ncbi", "--ref", "F1L3"])
genome_files = [
x for x in listdir(expanduser("~/.genome/F1L3")) if x != ".DS_Store"
]
print(genome_files)
assert len(genome_files) >= 11
def test_template():
if not os.path.exists(os.path.expanduser("~/.genome/WBcel235/WBcel235.fa.gz")):
genome.main(["genome","ncbi","--ref=WBcel235"])
with Capturing() as out:
primer.main(["primer", "template", "--size=500", "--ref=WBcel235","--region=I:1-100000", "test_data/test.vcf.gz"])
t = eval(str(out))[1].split("\t")[6][0:20]
assert t == "ATTTCCCTCTCCGGGAAATG"
def test_sanger():
if not os.path.exists(os.path.expanduser("~/.genome/WBcel235/WBcel235.fa.gz")):
genome.main(["genome","ncbi","--ref=WBcel235"])
with Capturing() as out:
primer.main(["primer", "sanger", "--ref=WBcel235","--region=I:542216-543215", "test_data/test.vcf.gz"])
t = eval(str(out))[1].split("\t")[8:10]
assert t == ['GAGAAGGACGGGACCCTTTG', 'aGGCCAGAACCTCGTGAAAC']
def test_snip():
if not os.path.exists(os.path.expanduser("~/.genome/WBcel235/WBcel235.fa.gz")):
genome.main(["genome","ncbi","--ref=WBcel235"])
with Capturing() as out:
primer.main(["primer", "snip", "--size=500", "--ref=WBcel235","--region=I:542216-543215", "test_data/test.vcf.gz"])
t = eval(str(out))[1].split("\t")[7:9]
assert t == ['496:496,184', '429,496:429,67,184']
def test_call_DL238():
if not os.path.exists(os.path.expanduser("~/.genome/WBcel235/WBcel235.fa.gz")):
genome.main(["genome","ncbi","--ref=WBcel235"])
with Capturing() as out:
call.main(["call", "test_data/DL238.ab1", "--ref=WBcel235", "--vcf-sites", "test_data/DL238.vcf.gz"])
out = eval(str(out))
assert len(out) == 5
out = out[1].split("\t")
assert out[0] == "X"
assert int(out[1]) == 14557228
assert out[2] == out[3]
assert out[5] == out[6]
assert out[9] == "TN"
def test_call_DL238():
if not os.path.exists(
os.path.expanduser("~/.genome/WBcel235/WBcel235.fa.gz")):
genome.main(["genome", "ncbi", "--ref=WBcel235"])
with Capturing() as out:
call.main([
"call", "test_data/DL238.ab1", "--ref=WBcel235", "--vcf-sites",
"test_data/DL238.vcf.gz"
])
out = eval(str(out))
assert len(out) == 5
out = out[1].split("\t")
assert out[0] == "X"
assert int(out[1]) == 14557228
assert out[2] == out[3]
assert out[5] == out[6]
assert out[9] == "TN"
def test_search_genome():
results = genome.main(["genome", "--search", "coli"])
search_result = [x for x in results if x[0] == "GCF_900042795.1"][0][3]
assert search_result == "F1L3"
def test_set_genome_location():
directory = genome.main(["genome", "location", "."])
assert directory == os.getcwd()
# Set genome location back to default
genome.main(["genome", "location", "-"])
def test_genome_location():
directory = genome.main(["genome", "location"])
assert os.path.exists(os.path.expanduser("~/.genome"))
def test_download_genome():
genome.main(["genome", "ncbi", "--ref", "F1L3"])
genome_files = [x for x in listdir(expanduser("~/.genome/F1L3")) if x != ".DS_Store"]
assert len(genome_files) == 11
def test_search_genome():
results = genome.main(["genome", "--search", "coli"])
search_result = [x for x in results if x[0] == "GCF_900042795.1"][0][3]
assert search_result == "F1L3"
def test_set_genome_location():
directory = genome.main(["genome","location", "."])
assert directory == os.getcwd()
# Set genome location back to default
genome.main(["genome","location", "-"])
def test_genome_location():
directory = genome.main(["genome","location"])
assert os.path.exists(os.path.expanduser("~/.genome"))