def is_transitive(A, B, C, windowsize=20, threshold=.5):
ab = paircomp.do_simple_nxn_compare(A, B, windowsize, threshold)
bc = paircomp.do_simple_nxn_compare(B, C, windowsize, threshold)
ac = paircomp.do_simple_nxn_compare(A, C, windowsize, threshold)
ac_tran1 = paircomp.build_transitive(ab, bc, A, C, threshold)
ac_tran2 = paircomp.filter_transitively(ab, bc, ac)[2]
assert ac_tran1 == ac_tran2
def test():
el = fasta.load_single(thisdir + 'el.txt')
br = fasta.load_single(thisdir + 'br.txt')
re = fasta.load_single(thisdir + 're.txt')
### first break the algorithms.
simple_cmp = None
try:
simple_cmp = paircomp.do_simple_nxn_compare("ATCCGRRRRUUUUU", br, 10, .5)
except:
pass
assert simple_cmp is None
# break on windowsizes
try:
simple_cmp = paircomp.do_simple_nxn_compare(el, br, -1, .5)
except:
pass
assert simple_cmp is None
try:
simple_cmp = paircomp.do_simple_nxn_compare(el, br, 256, .5)
except:
pass
assert simple_cmp is None
try:
# break on windowsizes in relation to sequence len
simple_cmp = paircomp.do_simple_nxn_compare("AAAAAAAAAAAAAAAAAAA",
br, 20, .5)
except:
pass
assert simple_cmp is None
try:
simple_cmp = paircomp.do_simple_nxn_compare(el, "AAAAAAAAAAAAAAAAAAA",
20, .5)
except:
pass
assert simple_cmp is None
# break on threshold
try:
simple_cmp = paircomp.do_simple_nxn_compare(el, br, 9, -.01)
except:
pass
assert simple_cmp is None
try:
simple_cmp = paircomp.do_simple_nxn_compare(el, br, 9, 1.01)
except:
pass
assert simple_cmp is None
simple_cmp_1 = paircomp.do_simple_nxn_compare(el, br, 20, .5)
simple_cmp_2 = paircomp.do_simple_nxn_compare(el, br, 22, .5)
result = None
try:
result = simple_cmp_1.contains(simple_cmp_2)
except:
pass
assert result is None
try:
result = simple_cmp_1.equals(simple_cmp_2)
except:
pass
assert result is None
try:
result = simple_cmp_1.subtract(simple_cmp_2)
except:
pass
assert result is None
try:
result = simple_cmp_1.intersect(simple_cmp_2)
except:
pass
assert result is None
### test transitivity stuff
windowsize = 20
threshold = 0.7
ab = paircomp.do_simple_nxn_compare(el, br, windowsize, threshold)
ab2 = paircomp.do_simple_nxn_compare(el, br, windowsize+1, threshold)
bc = paircomp.do_simple_nxn_compare(br, re, windowsize, threshold)
bc2 = paircomp.do_simple_nxn_compare(br, re, windowsize+1, threshold)
ac = paircomp.do_simple_nxn_compare(el, re, windowsize, threshold)
results = None
try:
results = paircomp.build_transitive(ab, bc, el, br, threshold)
except:
pass
assert results is None
try:
results = paircomp.build_transitive(ab, bc, br, re, threshold)
except Exception, e:
pass
results = None
try:
results = paircomp.build_transitive(ab, bc, el, br, threshold)
except:
pass
assert results is None
try:
results = paircomp.build_transitive(ab, bc, br, re, threshold)
except Exception, e:
pass
assert results is None
try:
results = paircomp.build_transitive(ab2, bc, el, re, threshold)
except:
pass
assert results is None
try:
results = paircomp.build_transitive(ab, bc2, el, re, threshold)
except:
pass
assert results is None
try:
results = paircomp.filter_transitively(ab2, bc, ac)
except:
pass
assert results is None
