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()