Python format_binary_sff примеры использования

Пример #1

def make_flow_txt(sff_fp, output_fp, use_sfftools=False):
    """Makes flowgram file from sff file."""
    if use_sfftools:
        check_sffinfo()
        _check_call(['sffinfo', sff_fp], stdout=open(output_fp, 'w'))
    else:
        format_binary_sff(open(sff_fp), open(output_fp, 'w'))

Пример #2

Файл: process_sff.py Проект: Ecogenomics/FrankenQIIME

def make_flow_txt(sff_fp, output_fp, use_sfftools=False):
    """Makes flowgram file from sff file."""
    if use_sfftools:
        check_sffinfo()
        _check_call(['sffinfo', sff_fp], stdout=open(output_fp, 'w'))
    else:
        try:
            format_binary_sff(open(sff_fp), open(output_fp, 'w'))
        except:
            raise IOError("Could not parse SFF %s" % sff_fp)

Пример #3

def make_flow_txt(sff_fp, output_fp, use_sfftools=False):
    """Makes flowgram file from sff file."""
    if use_sfftools:
        _fail_on_gzipped_sff(sff_fp)
        check_sffinfo()
        _check_call(['sffinfo', sff_fp], stdout=open(output_fp, 'w'))
    else:
        try:
            format_binary_sff(qiime_open(sff_fp, 'rb'), open(output_fp, 'w'))
        except:
            raise IOError("Could not parse SFF %s" % sff_fp)

Пример #4

Файл: test_binary_sff.py Проект: miklou/pycogent

 def test_format_binary_sff(self):
     output_buffer = format_binary_sff(open(SFF_FP))
     output_buffer.seek(0)
     expected = COMMON_HEADER_TXT + READ_HEADER_TXT + READ_DATA_TXT
     observed = output_buffer.read(len(expected))
     self.assertEqual(observed, expected)

Пример #5

Файл: test_binary_sff.py Проект: mikerobeson/pycogent

 def test_format_binary_sff(self):
     output_buffer = format_binary_sff(open(SFF_FP))
     output_buffer.seek(0)
     expected = COMMON_HEADER_TXT + READ_HEADER_TXT + READ_DATA_TXT
     observed = output_buffer.read(len(expected))
     self.assertEqual(observed, expected)