Example #1
0
 def __str__(self):
     from SAP.Bio._py3k import StringIO
     handle = StringIO()
     save(self, handle)
     handle.seek(0)
     return handle.read()
Example #2
0
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---- 
    ALEU_HORVU          MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG 
    CATH_HUMAN          ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
    CYS1_DICDI          -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
    ;
    end; 
    """)
    for a in NexusIterator(handle):
        print(a)
        for r in a:
            print("%r %s %s" % (r.seq, r.name, r.id))
    print("Done")
    print("")
    print("Reading an empty file")
    assert 0 == len(list(NexusIterator(StringIO())))
    print("Done")
    print("")
    print("Writing...")

    handle = StringIO()
    NexusWriter(handle).write_file([a])
    handle.seek(0)
    print(handle.read())

    handle = StringIO()
    try:
        NexusWriter(handle).write_file([a, a])
        assert False, "Should have rejected more than one alignment!"
    except ValueError:
        pass
Example #3
0
 def __str__(self):
     from SAP.Bio._py3k import StringIO
     handle = StringIO()
     save(self, handle)
     handle.seek(0)
     return handle.read()