def test_sum_bases_in_bins(self):
"""Test sum_bases_in_bins"""
scg_tsv = ospj(DATA_PATH, "sample0_gt500_scg.tsv")
b = sum_bases_in_bins(pd.read_csv(scg_tsv, sep="\t"),
ospj(DATA_PATH, "sample0_gt500.fa"))
assert_equal(12, b)
df = get_approved_bins(ospj(DATA_PATH, "sample0_gt500_scg.tsv"),
max_missing_scg=2, max_multicopy_scg=4)
b = sum_bases_in_bins(df, ospj(DATA_PATH, "sample0_gt500.fa"))
assert_equal(4, b)
def test_sum_bases_in_bins(self):
"""Test sum_bases_in_bins"""
scg_tsv = ospj(DATA_PATH, "sample0_gt500_scg.tsv")
b = sum_bases_in_bins(pd.read_csv(scg_tsv, sep="\t"),
ospj(DATA_PATH, "sample0_gt500.fa"))
assert_equal(12, b)
df = get_approved_bins(ospj(DATA_PATH, "sample0_gt500_scg.tsv"),
max_missing_scg=2,
max_multicopy_scg=4)
b = sum_bases_in_bins(df, ospj(DATA_PATH, "sample0_gt500.fa"))
assert_equal(4, b)
def test_write_approved_bins(self):
"""Test write_approved_bins"""
df = get_approved_bins(ospj(DATA_PATH, "sample0_gt500_scg.tsv"),
max_missing_scg=2, max_multicopy_scg=4)
assert_equal(2, int(df.Cluster))
write_approved_bins(df, ospj(DATA_PATH, "sample0_gt500.fa"),
TMP_BASENAME_DIR, "sample0_gt500")
ok_(os.path.exists(ospj(TMP_BASENAME_DIR, "sample0_gt500_bin2.fa")))
# make sure both have equal amount of records
assert_equal(
open(ospj(TMP_BASENAME_DIR, "sample0_gt500_bin2.fa")).read().count(">"),
open(ospj(DATA_PATH, "sample0_gt500_bin2.fa")).read().count(">"))
def test_write_approved_bins(self):
"""Test write_approved_bins"""
df = get_approved_bins(ospj(DATA_PATH, "sample0_gt500_scg.tsv"),
max_missing_scg=2,
max_multicopy_scg=4)
assert_equal(2, int(df.Cluster))
write_approved_bins(df, ospj(DATA_PATH, "sample0_gt500.fa"),
TMP_BASENAME_DIR, "sample0_gt500")
ok_(os.path.exists(ospj(TMP_BASENAME_DIR, "sample0_gt500_bin2.fa")))
# make sure both have equal amount of records
assert_equal(
open(ospj(TMP_BASENAME_DIR,
"sample0_gt500_bin2.fa")).read().count(">"),
open(ospj(DATA_PATH, "sample0_gt500_bin2.fa")).read().count(">"))
def test_get_approved_bins(self):
"""Test get_approved_bins"""
df = get_approved_bins(ospj(DATA_PATH, "sample0_gt500_scg.tsv"),
max_missing_scg=2,
max_multicopy_scg=4)
assert_equal(2, int(df.Cluster))
def test_get_approved_bins(self):
"""Test get_approved_bins"""
df = get_approved_bins(ospj(DATA_PATH, "sample0_gt500_scg.tsv"),
max_missing_scg=2, max_multicopy_scg=4)
assert_equal(2, int(df.Cluster))
