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src/q/i/qiime-1.8.0/qiime/process_sff.py   qiime(Download)
#!/usr/bin/env python
#file process_sff.py
from cogent.util.misc import app_path
from cogent.app.util import ApplicationNotFoundError
from cogent.parse.binary_sff import (
    else:
        try:
            format_binary_sff(qiime_open(sff_fp, 'rb'), open(output_fp, 'w'))
        except:
            raise IOError("Could not parse SFF %s" % sff_fp)

src/q/i/qiime-HEAD/qiime/process_sff.py   qiime(Download)
 
from skbio.app.util import ApplicationNotFoundError
from cogent.parse.binary_sff import (
    parse_binary_sff, format_binary_sff, write_binary_sff, decode_accession,
)
    else:
        try:
            format_binary_sff(qiime_open(sff_fp, 'rb'), open(output_fp, 'w'))
        except:
            raise IOError("Could not parse SFF %s" % sff_fp)

src/c/o/cogent-1.5.3/tests/test_parse/test_binary_sff.py   cogent(Download)
from unittest import TestCase, main
 
from cogent.parse.binary_sff import (
    seek_pad, parse_common_header, parse_read_header, parse_read_data,
    validate_common_header, parse_read, parse_binary_sff, UnsupportedSffError,
    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))

src/p/y/pycogent-HEAD/tests/test_parse/test_binary_sff.py   pycogent(Download)
from unittest import TestCase, main
 
from cogent.parse.binary_sff import (
    seek_pad, parse_common_header, parse_read_header, parse_read_data,
    validate_common_header, parse_read, parse_binary_sff, UnsupportedSffError,
    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))