def test_revcomp(self):
a=Dseqrecord("attt")
rc = a.rc()
self.assertTrue( str(rc.seq) == "aaat")
def test_revcomp(self):
a = Dseqrecord("attt")
rc = a.rc()
self.assertTrue(str(rc.seq) == "aaat")
def test_linear_circular(self):
''' test Dseqrecord linear & circular property'''
a=Dseqrecord("attt")
a.stamp()
self.assertTrue( a.verify_stamp() )
a=Dseqrecord("attt", linear = True)
self.assertTrue(a.linear == True)
self.assertTrue(a.circular == False)
self.assertTrue(a.rc().linear == True)
self.assertTrue(a.rc().circular == False)
self.assertTrue(a.seq.linear == True)
self.assertTrue(a.seq.circular == False)
a=Dseqrecord("attt", linear = False)
self.assertTrue(a.linear == False)
self.assertTrue(a.circular == True)
self.assertTrue(a.rc().linear == False)
self.assertTrue(a.rc().circular == True)
self.assertTrue(a.seq.linear == False)
self.assertTrue(a.seq.circular == True)
a=Dseqrecord("attt", circular = True)
self.assertTrue(a.linear == False)
self.assertTrue(a.circular == True)
self.assertTrue(a.rc().linear == False)
self.assertTrue(a.rc().circular == True)
self.assertTrue(a.seq.linear == False)
self.assertTrue(a.seq.circular == True)
a=Dseqrecord("attt", circular = False)
self.assertTrue(a.linear == True)
self.assertTrue(a.circular == False)
self.assertTrue(a.rc().linear == True)
self.assertTrue(a.rc().circular == False)
self.assertTrue(a.seq.linear == True)
self.assertTrue(a.seq.circular == False)
def test_linear_circular(self):
''' test Dseqrecord linear & circular property'''
a = Dseqrecord("attt")
a.stamp()
self.assertTrue(a.verify_stamp())
a = Dseqrecord("attt", linear=True)
self.assertTrue(a.linear == True)
self.assertTrue(a.circular == False)
self.assertTrue(a.rc().linear == True)
self.assertTrue(a.rc().circular == False)
self.assertTrue(a.seq.linear == True)
self.assertTrue(a.seq.circular == False)
a = Dseqrecord("attt", linear=False)
self.assertTrue(a.linear == False)
self.assertTrue(a.circular == True)
self.assertTrue(a.rc().linear == False)
self.assertTrue(a.rc().circular == True)
self.assertTrue(a.seq.linear == False)
self.assertTrue(a.seq.circular == True)
a = Dseqrecord("attt", circular=True)
self.assertTrue(a.linear == False)
self.assertTrue(a.circular == True)
self.assertTrue(a.rc().linear == False)
self.assertTrue(a.rc().circular == True)
self.assertTrue(a.seq.linear == False)
self.assertTrue(a.seq.circular == True)
a = Dseqrecord("attt", circular=False)
self.assertTrue(a.linear == True)
self.assertTrue(a.circular == False)
self.assertTrue(a.rc().linear == True)
self.assertTrue(a.rc().circular == False)
self.assertTrue(a.seq.linear == True)
self.assertTrue(a.seq.circular == False)
def test_map(self):
traces = []
import glob
for name in glob.glob('*.ab1'):
traces.append( abiread( name, "abi") )
for t in traces:
d = Dseqrecord(t.seq)
if "ITVFFKEYPYDVPDYAIEGIFHAT" in d:
tag = "tat cca tat gac gtt cca gac tat gca"
trc = "ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag,trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue( str( s[sl].seq.translate() ) == "YPYDVPDYA")
self.assertTrue( "YPYDVPDYA" in s)
tag = "AAA tat cca tat gac gtt cca gac tat gca"
trc = " ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag,trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue( str( s[sl].seq.translate() ) == "YPYDVPDYA" )
self.assertTrue( "YPYDVPDYA" in s )
tag = " tat cca tat gac gtt cca gac tat gca"
trc = "AAA ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag,trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue( str( s[sl].seq.translate() ) == "YPYDVPDYA" )
self.assertTrue( "YPYDVPDYA" in s )
tag = " tat cca tat gac gtt cca gac tat gca"
trc = "AAA ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag,trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue( str( s[sl].seq.translate() ) == "YPYDVPDYA" )
tag = "tat cca tat gac gtt cca gac tat gca"
trc = "ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
tag, trc = trc, tag
s = Dseqrecord(Dseq(tag,trc))
sl = s.rc().find_aa("YPYDVPDYA")
self.assertTrue( str( s.rc()[sl].seq.translate()) == "YPYDVPDYA" )
self.assertTrue( "YPYDVPDYA" in s.rc() )
tag = "aaa tat cca tat gac gtt cca gac tat gca"
trc = "ttt ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag,trc, circular=True))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue( str( s[sl].seq.translate() ) == "YPYDVPDYA" )
self.assertTrue( "YPYDVPDYA" in s )
def test_map(self):
traces = []
import glob
for name in glob.glob('*.ab1'):
traces.append(abiread(name, "abi"))
for t in traces:
d = Dseqrecord(t.seq)
if "ITVFFKEYPYDVPDYAIEGIFHAT" in d:
tag = "tat cca tat gac gtt cca gac tat gca"
trc = "ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
tag = "AAA tat cca tat gac gtt cca gac tat gca"
trc = " ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
tag = " tat cca tat gac gtt cca gac tat gca"
trc = "AAA ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
tag = " tat cca tat gac gtt cca gac tat gca"
trc = "AAA ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
tag = "tat cca tat gac gtt cca gac tat gca"
trc = "ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
tag, trc = trc, tag
s = Dseqrecord(Dseq(tag, trc))
sl = s.rc().find_aa("YPYDVPDYA")
self.assertTrue(str(s.rc()[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s.rc())
tag = "aaa tat cca tat gac gtt cca gac tat gca"
trc = "ttt ata ggt ata ctg caa ggt ctg ata cgt"[::-1]
s = Dseqrecord(Dseq(tag, trc, circular=True))
sl = s.find_aa("YPYDVPDYA")
self.assertTrue(str(s[sl].seq.translate()) == "YPYDVPDYA")
self.assertTrue("YPYDVPDYA" in s)
