def test_show_help(capsys):
"""
Show help.
Arguments:
capsys: Pytest fixture to capture output.
"""
with pytest.raises(SystemExit):
cli.main(["-h"])
captured = capsys.readouterr()
assert "kmer_counter" in captured.out
def test_background(capsys):
res = {
'GCA': 7,
'CAC': 16,
'ACC': 15,
'CCA': 14,
'ACG': 3,
'GCG': 12,
'GCC': 24,
'CCC': 14,
'CAG': 11,
'GCT': 7,
'TAG': 8,
'TAA': 6,
'AAT': 5,
'AAA': 8,
'ACT': 4,
'TAC': 1,
'TCT': 4,
'GAG': 9,
'GAT': 12,
'CAT': 1,
'AAC': 5,
'GAA': 1,
'GAC': 3,
'TCA': 12,
'CAA': 8,
'TCC': 9,
'CCT': 16,
'AAG': 5,
'CCG': 16,
'ACA': 3,
'TAT': 1,
}
assert(cli.main(["background","tests/data/test.2bit","--bed", "tests/data/bg_test.bed","-r1"])==0)
captured = capsys.readouterr()
D = {}
for line in captured.out.split('\n'):
if line == "":
continue
kmer, count = line.split(" ")
assert res[kmer] == int(count)
def test_snv(capsys):
res = {
'GAT': 1,
'CCC': 1,
'CAA': 1,
'TCC': 1,
'AAA': 1,
'GCG': 2,
'CCA': 2,
'GCA': 1,
'ACC': 2,
'CCG': 1
}
assert(cli.main(["snv","tests/data/test.2bit","tests/data/pos_test.txt","-r1"])==0)
captured = capsys.readouterr()
D = {}
for line in captured.out.split('\n'):
if line == "":
continue
kmer, count = line.split(" ")
assert res[kmer] == int(count)
"""
Entry-point module, in case you use `python -m kmer_counter`.
"""
import sys
from kmer_counter.cli import main
if __name__ == "__main__":
sys.exit(main(sys.argv[1:]))
def test_main():
"""Basic CLI test."""
assert cli.main([]) == 0