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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 (
        header, reads = adjust_sff_cycles(parse_binary_sff(qiime_open(sff_fp, 'rb'),
                                          True), 100)
        write_binary_sff(open(output_fp, 'w'), header, reads)
 
 

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,
)
            parse_binary_sff(qiime_open(sff_fp, 'rb'),
                             True), 100)
        write_binary_sff(open(output_fp, 'w'), header, reads)
 
 

src/q/i/qiime-1.8.0/qiime/trim_sff_primers.py   qiime(Download)
from cogent.app.util import ApplicationNotFoundError
from qiime.parse import parse_mapping_file
from cogent.parse.binary_sff import (
    parse_binary_sff, write_binary_sff
    )
        _, temp_fp = tempfile.mkstemp(dir=sff_dir)
        with open(temp_fp, 'w') as f:
            write_binary_sff(f, clipped_header, clipped_reads)
 
        shutil.move(temp_fp, sff_fp)

src/q/i/qiime-HEAD/qiime/trim_sff_primers.py   qiime(Download)
 
from skbio.app.util import ApplicationNotFoundError
from cogent.parse.binary_sff import parse_binary_sff, write_binary_sff
from skbio.app.util import which
 
        close(fd)
        with open(temp_fp, 'w') as f:
            write_binary_sff(f, clipped_header, clipped_reads)
 
        move(temp_fp, sff_fp)

src/q/i/qiime-1.8.0/qiime/make_per_library_sff.py   qiime(Download)
    check_sfffile,
    )
from cogent.parse.binary_sff import (
    parse_binary_sff, write_binary_sff,
    )
    if debug:
        print 'Creating SFF file for %s' % id_list_fp
    write_binary_sff(open(output_fp, 'w'), *filtered_sff_data)
 
 

src/q/i/qiime-HEAD/qiime/make_per_library_sff.py   qiime(Download)
    check_sfffile,
)
from cogent.parse.binary_sff import (
    parse_binary_sff, write_binary_sff,
)
    if debug:
        print 'Creating SFF file for %s' % id_list_fp
    write_binary_sff(open(output_fp, 'w'), *filtered_sff_data)
 
 

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,
        header['number_of_reads'] = 1
 
        write_binary_sff(self.output_file, header, [read])
 
        file_pos = self.output_file.tell()

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,
        header['number_of_reads'] = 1
 
        write_binary_sff(self.output_file, header, [read])
 
        file_pos = self.output_file.tell()

src/q/i/qiime-HEAD/tests/test_trim_sff_primers.py   qiime(Download)
 
from unittest import TestCase, main
from cogent.parse.binary_sff import (
    parse_binary_sff, write_binary_sff,
)

src/q/i/qiime-1.8.0/tests/test_trim_sff_primers.py   qiime(Download)
 
from cogent.util.unit_test import TestCase, main
from cogent.parse.binary_sff import (
    parse_binary_sff, write_binary_sff,
    )