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'))
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)
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)
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)