def test_commandline(capsys,tmpdir):
d = tmpdir.mkdir('dir')
f = d.join('forward.txt')
r = d.join('reverse.txt')
o = d.join('output.txt')
f.write("3 10 20 24 49")
r.write("30 42 51 90\n\n")
__main__.main(['-f',str(f),'-r',str(r),'-o',str(o)])
o2 = d.join('output2.txt')
os.system('ampcount -f '+str(f)+' -r '+str(r)+' -o '+str(o2))
assert o.read() == o2.read()
o3 = d.join('output3.txt')
os.system('python -m ampcountpy -f '+str(f)+' -r '+str(r)+' -o '+str(o3))
assert o.read() == o3.read()
def test_main(capsys,tmpdir):
with pytest.raises(SystemExit):
__main__.main()
out, err=capsys.readouterr()
assert 'usage' in err
with pytest.raises(SystemExit):
__main__.main(['-h'])
out, err=capsys.readouterr()
assert 'usage' in out
d = tmpdir.mkdir('dir')
f = d.join('forward.txt')
r = d.join('reverse.txt')
o = d.join('output.txt')
f.write("1 10 20")
r.write("")
__main__.main(['-f',str(f),'-r',str(r),'-o',str(o)])
out=o.read().split('\n')[1:]
amps=[int(x.split(',')[2]) for x in out if len(x)>0]
assert all([x==y for x,y in zip(amps,[1,2,3,2,1])])
r.write("30 42 51\n\n")
__main__.main(['-f',str(f),'-r',str(r),'-o',str(o)])
out=o.read().split('\n')[1:]
amps=[int(x.split(',')[2]) for x in out if len(x)>0]
assert max(amps)==38
#check start ends and max length
__main__.main(['-f',str(f),'-r',str(r),'-o',str(o),'-l',str(100)])
out=[x for x in o.read().split('\n')[1:] if len(x)>0]
assert int(out[0].split(',')[0])==1
assert int(out[-1].split(',')[1])==119
#check max genome size
__main__.main(['-f',str(f),'-r',str(r),'-o',str(o),'-l',str(100),'-g',str(60)])
out=[x for x in o.read().split('\n')[1:] if len(x)>0]
assert int(out[0].split(',')[0])==1
assert int(out[-1].split(',')[1])==60
amps=[int(x.split(',')[2]) for x in out if len(x)>0]
assert max(amps)==38
__main__.main(['-f',str(f),'-r',str(r),'-o',str(o),'-v'])
out, err=capsys.readouterr()
