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src/b/i/biopython-1.63/Tests/test_AlignIO_convert.py   biopython(Download)
    handle2 = StringIO()
    try:
        count2 = AlignIO.convert(in_filename, in_format, handle2, out_format, alphabet)
    except ValueError:
        count2 = 0
    handle2 = StringIO()
    try:
        count2 = AlignIO.convert(open(in_filename), in_format, handle2, out_format, alphabet)
    except ValueError:
        count2 = 0

src/b/i/biopython-HEAD/Tests/test_AlignIO_convert.py   biopython(Download)
    handle2 = StringIO()
    try:
        count2 = AlignIO.convert(in_filename, in_format, handle2, out_format, alphabet)
    except ValueError:
        count2 = 0
    try:
        with open(in_filename) as handle1:
            count2 = AlignIO.convert(handle1, in_format, handle2, out_format, alphabet)
    except ValueError:
        count2 = 0

src/b/i/biopython-1.63/Tests/test_EmbossPhylipNew.py   biopython(Download)
def write_AlignIO_dna():
    """Convert opuntia.aln to a phylip file"""
    assert 1 == AlignIO.convert("Clustalw/opuntia.aln", "clustal",
                                "Phylip/opuntia.phy", "phylip")
 
 
def write_AlignIO_protein():
    """Convert hedgehog.aln to a phylip file"""
    assert 1 == AlignIO.convert("Clustalw/hedgehog.aln", "clustal",

src/b/i/biopython-HEAD/Tests/test_EmbossPhylipNew.py   biopython(Download)
def write_AlignIO_dna():
    """Convert opuntia.aln to a phylip file"""
    assert 1 == AlignIO.convert("Clustalw/opuntia.aln", "clustal",
                                "Phylip/opuntia.phy", "phylip")
 
 
def write_AlignIO_protein():
    """Convert hedgehog.aln to a phylip file"""
    assert 1 == AlignIO.convert("Clustalw/hedgehog.aln", "clustal",