def test1(filename):
algn = core.Alignment(
sequence_utils.read_sequence(filename), name = "pTAK117", type = "PLASMID")
print sequence_utils.format_sequence(algn.sequence())
print algn.is_cyclic()
print algn.size()
print algn.annotations()
print algn.sequence(1, 10, +1)
print algn.sequence(10, 20, +1)
print algn.sequence(6080, 10, +1)
print algn.sequence(20, 10, -1)
print algn.sequence(10, 6080, -1)
def test2(filename):
algn = core.Alignment(
sequence_utils.read_sequence(filename), name = "pTAK117", type = "PLASMID")
print "Ptrc", algn.sequence(11, 98, +1)
print "PL-s1con", algn.sequence(6067, 5496, -1)
print "CI", algn.sequence(99, 714, +1)
print "GFP", algn.sequence(914, 1630, +1)
print "LacI", algn.sequence(5489, 4407, -1)
# print "rbs E", algn.sequence(87, 101, +1)
# print "rbs B", algn.sequence(894, 907, +1)
print "rrn T1", algn.sequence(1846, 1889, +1)
print "rrn T2", algn.sequence(2021, 2048, +1)
print "rrn T1", algn.sequence(-1903, -1946, -1)
print "rrn T2", algn.sequence(-2078, -2105, -1)
print "TSS1", algn.sequence(60, 60, +1)
print "TSS2", algn.sequence(-94, -94, -1)
print "Olac", algn.sequence(60, 81, +1)
print "OL3", algn.sequence(6061, 6045, -1)
print "OL2", algn.sequence(6040, 6025, -1)
print "OL1", algn.sequence(6016, 6001, -1)
def test3(filename):
algn = core.Alignment(
sequence_utils.read_sequence(filename), name = "pTAK117", type = "PLASMID")
trk = core.Track(algn.size(), algn.is_cyclic())
trk.place_domain(domain.Domain("A"), 1)
trk.place_domain(domain.Domain("B"), 2)
trk.place_domain(domain.Domain("A"), 3)
print trk.list_domains()
print trk.states()[: 10]
print "removed", trk.remove_domain(1)
print trk.list_domains()
print trk.states()[: 10]
print "removed", trk.remove_domain(2)
print trk.list_domains()
print trk.states()[: 10]
trk.place_domain(domain.Domain("C"), 1)
trk.place_domain(domain.Domain("C"), 2)
print trk.list_domains()
print trk.states()[: 10]
print trk.query_domains_by_region(1, 2, +1)
print trk.query_domains_by_region(1, 3, +1)
trk.place_domain(domain.Domain("D"), 4, 8, +1)
print trk.states()[: 10], trk.list_domains()
