Ejemplo n.º 1
0
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
Ejemplo n.º 2
0
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