def test():
el = fasta.load_single(thisdir + 'el.txt')
br = fasta.load_single(thisdir + 'br.txt')
re = fasta.load_single(thisdir + 're.txt')
print 'testing comparison:'
print 'GC\tloop count'
for i in range(0, 100):
if i % 10 == 0:
print gc.collect(), '\t', i
cmp = paircomp.do_rolling_nxn_compare(el, br, 20, .5)
### test transitivity, too.
ab = paircomp.do_rolling_nxn_compare(el, br, 20, .7)
bc = paircomp.do_rolling_nxn_compare(br, re, 20, .7)
ac = paircomp.do_rolling_nxn_compare(el, re, 20, .7)
print 'testing transitivity:'
print 'GC\tloop count'
for i in range(0, 100):
if i % 10 == 0:
print gc.collect(), '\t', i
(new_ab, new_bc, new_ac) = paircomp.filter_transitively(ab, bc, ac)
del new_ab, new_bc, new_ac
del ab, bc, ac
print 'remaining objects to collect:'
print gc.collect()
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():
t1 = fasta.load_single(thisdir + 't1.fa', force='DNA')
t2 = fasta.load_single(thisdir + 't2.fa', force='DNA')
t3 = fasta.load_single(thisdir + 't3.fa', force='DNA')
AB = paircomp.do_simple_nxn_compare(t1, t2, 4, 1.0)
BC = paircomp.do_simple_nxn_compare(t2, t3, 4, 1.0)
AC = paircomp.do_simple_nxn_compare(t1, t3, 4, 1.0)
(new_AB, new_BC, new_AC) = paircomp.filter_transitively(AB, BC, AC)
#print_cmp(new_AB)
#print_cmp(new_BC)
#print_cmp(new_AC)
expected = \
"""
4:0,0,20
4:0,0,-5
4:0,29,20
4:0,29,-5
4:0,-16,-5
4:0,-16,20
4:33,6,33
4:33,6,-33
4:33,43,33
4:33,43,-33
4:33,-43,-33
4:33,-43,33
4:33,-6,-33
4:33,-6,33\
"""
print 'Comparing paircomp output to Mussa\'s...',
l = print_tristan_3way(new_AB, new_BC, new_AC)
l.sort()
l2 = parse_tristan_3way(expected)
l2.sort()
assert l == l2
print 'success'
if l != l2:
print 'DIFF: CTB'
for x in l:
if not x in l2:
print x
print 'vs TDB'
for x in l2:
if not x in l:
print x
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
try:
results = paircomp.filter_transitively(ab, bc2, ac)
except:
pass
assert results is None
print 'SUCCESS.'
