def test(self): el = self.el br = self.br el_path = self.el_path br_path = self.br_path ### four different ways of doing analyses: # # execute paircomp # outname = 'el-br-0.5.p.cmp' os.system('rm %s >& /dev/null' % (outname,)) os.system('%s/paircomp %s %s 20 .5 %s >& /dev/null' % \ (bindir, self.el_path, self.br_path, outname)) p_cmp = paircomp.parse_paircomp(open(outname).read(), len(el), len(br), 20) os.system('rm %s >& /dev/null' % (outname,)) # # execute seqcomp # outname = 'el-br-0.5.s.cmp' os.system('rm %s >& /dev/null' % (outname,)) os.system('%s/seqcomp %s %s 20 10 noxml %s >& /dev/null' % \ (bindir, el_path, br_path, outname)) s_cmp = paircomp.parse_seqcomp(open(outname).read(), len(el), len(br), 20) os.system('rm %s >& /dev/null' % (outname,)) # # & use the python interface. # rolling_cmp = self.cmp simple_cmp = paircomp.do_simple_nxn_compare(el, br, 20, .5) ## also load in an old analysis for regression testing old_paircomp = paircomp.parse_paircomp(open('%s/orig-el-br.txt' % \ (thisdir,)).read(), len(el), len(br), 20) ## check to make sure they all return the same result! print 'Testing equality of internal vs external analyses...', assert p_cmp == s_cmp assert p_cmp == simple_cmp assert p_cmp == rolling_cmp assert p_cmp == old_paircomp
def test_round_trip(self): "round-trip both formats" el, br = self.el, self.br cmp = self.cmp print 'Testing save/load round-trip...' cmp.save('simple.cmp') simple_cmp_2 = paircomp.parse_paircomp(open('simple.cmp').read(), len(el), len(br), 20) assert cmp == simple_cmp_2 os.system('rm simple.cmp') cmp.save_as_seqcomp('simple_seqcomp.cmp') r = open('simple_seqcomp.cmp').read() simple_cmp_3 = paircomp.parse_seqcomp(r, len(el), len(br), 20) assert cmp == simple_cmp_3