def test_rename_combo():
comm = "vk rename --prefix PREFIX_ --suffix _SUFFIX --subst N2:TEST --subst WN2001,TEST2 --subst AB1=TEST3 test_data/test.vcf.gz | bcftools query --list-samples"
rename.main(["rename","--prefix","PREFIX_","--suffix","_SUFFIX","--subst","N2:TEST","--subst","WN2001,TEST2","--subst","AB1=TEST3","test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert all([x.startswith("PREFIX_") for x in out.splitlines()])
assert sum(["TEST" in x for x in out.splitlines()]) == 3
assert all([x.endswith("_SUFFIX") for x in out.splitlines()])
def test_rename_combo():
comm = "vk rename --prefix PREFIX_ --suffix _SUFFIX --subst N2:TEST --subst WN2001,TEST2 --subst AB1=TEST3 test_data/test.vcf.gz | bcftools query --list-samples"
rename.main(["rename","--prefix","PREFIX_","--suffix","_SUFFIX","--subst","N2:TEST","--subst","WN2001,TEST2","--subst","AB1=TEST3","test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert all([x.startswith("PREFIX_") for x in out.decode("utf-8").splitlines()])
assert sum(["TEST" in x for x in out.decode("utf-8").splitlines()]) == 3
assert all([x.endswith("_SUFFIX") for x in out.decode("utf-8").splitlines()])
def test_rename_prefix():
comm = "vk rename --prefix prefix_ data/test.vcf.gz | bcftools query --list-samples"
# Run 2x for testing
rename.main(["rename","--prefix","prefix_","test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert all([x.startswith("prefix") for x in out.splitlines()])
def test_rename_subst():
comm = "vk rename --subst N2:TEST --subst WN2001,TEST2 --subst AB1=TEST3 test_data/test.vcf.gz | bcftools query --list-samples"
rename.main(["rename","--subst","N2:TEST","--subst","WN2001,TEST2","--subst","AB1=TEST3", "test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert sum([x.startswith("TEST") for x in out.decode("utf-8").splitlines()]) == 3
def test_rename_suffix():
comm = "vk rename --suffix _suffix data/test.vcf.gz | bcftools query --list-samples"
rename.main(["rename","--suffix","_suffix","test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert all([x.endswith("_suffix") for x in out.splitlines()])
def test_rename_prefix():
comm = "vk rename --prefix prefix_ data/test.vcf.gz | bcftools query --list-samples"
# Run 2x for testing
rename.main(["rename","--prefix","prefix_","test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert all([x.startswith("prefix") for x in out.splitlines()])
def test_rename_subst():
comm = "vk rename --subst N2:TEST --subst WN2001,TEST2 --subst AB1=TEST3 test_data/test.vcf.gz | bcftools query --list-samples"
rename.main(["rename","--subst","N2:TEST","--subst","WN2001,TEST2","--subst","AB1=TEST3", "test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert sum([x.startswith("TEST") for x in out.splitlines()]) == 3
def test_rename_suffix():
comm = "vk rename --suffix _suffix data/test.vcf.gz | bcftools query --list-samples"
rename.main(["rename","--suffix","_suffix","test_data/test.vcf.gz"])
out, err = Popen(comm, stdout=PIPE, stderr=PIPE, shell=True).communicate()
assert all([x.endswith("_suffix") for x in out.splitlines()])