def test_commandline(capsys, bamFile):
getstartends.main([str(bamFile)])
out, err = capsys.readouterr()
out2 = subprocess.check_output("getstartends " + str(bamFile), shell=True)
out3 = subprocess.check_output("python -m dnapy.getstartends " +
str(bamFile),
shell=True)
for ii, jj, kk in zip(out.split('\n'),
out2.decode().split('\n'),
out3.decode().split('\n')):
print(ii)
print(jj)
assert ii == jj == kk
def test_main(capsys, tmpdir, bamFile):
with pytest.raises(SystemExit):
getstartends.main()
out, err = capsys.readouterr()
assert 'usage' in err
with pytest.raises(SystemExit):
getstartends.main(['-h'])
out, err = capsys.readouterr()
assert 'usage' in out
getstartends.main(['-v', str(bamFile)])
out, err = capsys.readouterr()
assert 'Arguments' in err
compare = getstartends.getStartsInFile(str(bamFile))
count = 0
for ii, jj in zip(out.split('\n')[1:], compare):
ii = ii.split(',')
count += 1
assert ii[0] == jj['ref']
assert int(ii[1]) == jj['start']
assert int(ii[2]) == jj['end']
assert ii[3] == jj['strand']
assert count == 2
compare = getstartends.getStartsInFile(str(bamFile), maxGaps=10)
getstartends.main([str(bamFile), '-g 10'])
out, err = capsys.readouterr()
count = 0
for ii, jj in zip(out.split('\n')[1:], compare):
count += 1
ii = ii.split(',')
assert ii[0] == jj['ref']
assert int(ii[1]) == jj['start']
assert int(ii[2]) == jj['end']
assert ii[3] == jj['strand']
assert count == 3
getstartends.main([str(bamFile), '-g 10', '-n'])
noHead, err = capsys.readouterr()
for ii, jj in zip(out.split('\n')[1:], noHead.split('\n')):
assert ii == jj
getstartends.main([str(bamFile), '-g 10', '-n', '-c'])
regCol, err = capsys.readouterr()
for ii, jj in zip(out.split('\n')[1:], regCol.split('\n')):
if ii:
ii = "None," + ii
assert ii == jj
getstartends.main([str(bamFile), '-g 10', '-n', '-c', '-r', 'ref:1-100'])
regCol, err = capsys.readouterr()
for ii, jj in zip(out.split('\n')[1:], regCol.split('\n')):
if ii:
ii = "ref:1-100," + ii
assert ii == jj
d = tmpdir.mkdir('dir')
p = d.join('test.regions')
p.write("ref:1-10\nref:1-100")
getstartends.main([str(bamFile), '-g 10', '-n', '-c', '-f', str(p)])
fileOut, err = capsys.readouterr()
for ii, jj in zip(regCol.split('\n'), fileOut.split('\n')):
assert ii == jj