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 do_3way_regression(a, b, c, windowsize, threshold):
"""
Run the current paircomp 3-way and return it in a similar
path format for comparison purposes.
"""
ab = paircomp.do_rolling_nxn_compare(a, b, windowsize, threshold)
bc = paircomp.do_rolling_nxn_compare(b, c, windowsize, threshold)
ac = paircomp.do_rolling_nxn_compare(a, c, windowsize, threshold)
(ab, bc, ac) = paircomp.parser.filter_transitively(ab, bc, ac)
paths = []
for i in range(0, len(a)):
matches = ab[i]
for m in matches:
bot = m.bot
if m.orientation == -1:
bot = bot - windowsize + 1
apos = _PosO(i, -1)
else:
apos = _PosO(i, 1)
matches2 = bc[bot]
for m2 in matches2:
bpos = _PosO(bot, m2.orientation)
if m2.orientation == -1:
cpos = _PosO(m2.bot - windowsize + 1, 1)
else:
cpos = _PosO(m2.bot, 1)
paths += [ [apos, bpos, cpos] ]
paths.sort()
return paths
def test():
thresh = 14.0/21
A='tttttttttttttttttttttttttttttttttttttttttttttttttt'
B='tttttttttttttttttttttttttttttttttttttttttttttttttt'
C='tttttttttttttttttttttttttttttttttttttttttttttttttt'
AB=paircomp.do_rolling_nxn_compare(A, B, 21, thresh)
BC=paircomp.do_rolling_nxn_compare(B, C, 21, thresh)
AC=paircomp.do_rolling_nxn_compare(A, C, 21, thresh)
a=time.time()
tran=paircomp.parser.filter_transitively(AB,BC,AC)
b=time.time()
print 'A B C are same '+str(b-a)
def setup(self):
self.el_path = os.path.join(thisdir, 'el.txt')
self.br_path = os.path.join(thisdir, 'br.txt')
self.el = fasta.load_single(self.el_path)
self.br = fasta.load_single(self.br_path)
self.cmp = paircomp.do_rolling_nxn_compare(self.el, self.br, 20, .5)
def test():
# construct a quick seqcomp
el = fasta.load_single(thisdir + "el.txt")
br = fasta.load_single(thisdir + "br.txt")
a = do_rolling_nxn_compare(el, br, 50, 0.5)
b = a.isolate_matching_bases(el, br)
print "test-1bp-matches.py PASSED."
def add_sequence(self, seq):
"""
"""
n = len(self.seqs)
for i in range(0, n):
cmp = paircomp.do_rolling_nxn_compare(self.seqs[i], seq,
self.windowsize,
self.threshold)
d = self.cmps.get(i, {})
d[n] = cmp
self.cmps[i] = d
self.seqs.append(seq)
#! /usr/bin/env python import sys import fasta import paircomp top = fasta.load_single(sys.argv[1]) bot = fasta.load_single(sys.argv[2]) windowsize = int(sys.argv[3]) threshold = float(sys.argv[4]) outfile = sys.argv[5] cmp = paircomp.do_rolling_nxn_compare(top, bot, windowsize, threshold) cmp.save(outfile)
