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src/b/i/biopython-1.63/Bio/AlignIO/NexusIO.py   biopython(Download)
    NexusWriter(handle).write_file([a])
    handle.seek(0)
    print(handle.read())
 
    handle = StringIO()

src/b/i/biopython-HEAD/Bio/AlignIO/NexusIO.py   biopython(Download)
    NexusWriter(handle).write_file([a])
    handle.seek(0)
    print(handle.read())
 
    handle = StringIO()

src/b/i/biopython-1.63/Bio/MarkovModel.py   biopython(Download)
        save(self, handle)
        handle.seek(0)
        return handle.read()
 
 

src/b/i/biopython-HEAD/Bio/MarkovModel.py   biopython(Download)
        save(self, handle)
        handle.seek(0)
        return handle.read()
 
 

src/b/i/biopython-HEAD/Tests/test_SeqIO_QualityIO.py   biopython(Download)
            with open("Quality/%s_as_%s.fastq" % (base_name, out_variant),
                      _universal_read_mode) as handle:
                expected = handle.read()
 
            with warnings.catch_warnings():

src/b/i/biopython-HEAD/Tests/test_AlignIO.py   biopython(Download)
                handle.seek(0)
                raise ValueError("%s\n\n%s\n\n%s"
                                  % (str(e), repr(handle.read()), repr(alignments2)))
            simple_alignment_comparison(alignments, alignments2, format)
 
                handle.seek(0)
                raise ValueError("%s\n\n%s\n\n%s"
                                  % (str(e), repr(handle.read()), repr(alignments2)))
            simple_alignment_comparison(alignments, alignments2, format)
 
        #print(" Trying to read a triple concatenation of the input file")
        with open(t_filename, "r") as handle:
            data = handle.read()
        handle = StringIO()
        handle.write(data + "\n\n" + data + "\n\n" + data)

src/b/i/biopython-1.63/Tests/test_SeqIO_QualityIO.py   biopython(Download)
            with open("Quality/%s_as_%s.fastq"
                      % (base_name, out_variant), "rU") as handle:
                expected = handle.read()
            #Check matches using convert...
            handle = StringIO()

src/b/i/biopython-1.63/Tests/test_AlignIO.py   biopython(Download)
                handle.seek(0)
                raise ValueError("%s\n\n%s\n\n%s"
                                  % (str(e), repr(handle.read()), repr(alignments2)))
            simple_alignment_comparison(alignments, alignments2, format)
 
                handle.seek(0)
                raise ValueError("%s\n\n%s\n\n%s"
                                  % (str(e), repr(handle.read()), repr(alignments2)))
            simple_alignment_comparison(alignments, alignments2, format)