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 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():
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
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."
import sys
## import local Fasta-format library.
sys.path.append('../tests/')
import fasta
if len(sys.argv) != 6:
sys.stderr.write("""Usage:
%s top_seq bot_seq paircomp_file windowsize threshold
""" % (sys.argv[0],))
sys.exit(-1)
top_seq = fasta.load_single(sys.argv[1])
bot_seq = fasta.load_single(sys.argv[2])
paircomp_file = open(sys.argv[3])
windowsize = int(sys.argv[4])
threshold = float(sys.argv[5])
print """
<Start>
<First>
<Sequence name="top sequence">
%s
</Sequence>
<!-- top sequence annotations can go here -->
</First>
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
#! /usr/bin/env python
import sys
sys.path.append('/u/t/dev/motility/python/build/lib.linux-i686-2.3/')
import motility
sys.path.append('/u/t/dev/slippy/lib')
import fasta
if len(sys.argv) != 3:
sys.stderr.write('Usage:\n\t%s <motif> <FASTA file to search>\n' % (sys.argv[0],))
sys.exit(0)
motif = sys.argv[1]
filename = sys.argv[2]
sys.stderr.write('searching file %s with motif %s\n' % (filename, motif,))
seq = fasta.load_single(filename)
results = motility.find_iupac(seq, motif)
for (start, end, orientation, match) in results:
print 'MATCH: %d --> %d, orientation %d; match is %s' % (start, end,
orientation,
match,)
sys.exit(0)
#! /usr/bin/env python
import sys, os, gc
import paircomp, fasta
A = "A"*21
B = "T"*21
dirname = os.path.dirname(__file__)
thisdir = os.path.normpath(dirname) + '/'
bindir = os.path.join(thisdir, '../../bin/')
el = fasta.load_single(thisdir + 'el.txt')
br = fasta.load_single(thisdir + 'br.txt')
re = fasta.load_single(thisdir + 're.txt')
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():
is_transitive(A, A, A)
is_transitive(A, A, B)
is_transitive(A, B, A)
#! /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_simple_nxn_compare(top, bot, windowsize, threshold) cmp.save(outfile)