Python inflate_denoiser_output Examples

Example #1

File: inflate_denoiser_output.py Project: Ecogenomics/FrankenQIIME

def main():
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    centroid_seqs = [MinimalFastaParser(open(e, "U")) for e in opts.centroid_fps.split(",")]
    singleton_seqs = [MinimalFastaParser(open(e, "U")) for e in opts.singleton_fps.split(",")]
    fasta_seqs = [MinimalFastaParser(open(e, "U")) for e in opts.fasta_fps.split(",")]
    denoiser_map_fs = [open(e, "U") for e in opts.denoiser_map_fps.split(",")]
    output_fasta_fp = opts.output_fasta_fp

    output_f = open(opts.output_fasta_fp, "w")
    for s in inflate_denoiser_output(
        chain.from_iterable(centroid_seqs),
        chain.from_iterable(singleton_seqs),
        chain.from_iterable(denoiser_map_fs),
        chain.from_iterable(fasta_seqs),
    ):
        output_f.write(">%s\n%s\n" % s)
    output_f.close()

Example #2

def main():
    option_parser, opts, args =\
        parse_command_line_parameters(**script_info)

    centroid_seqs = \
        [parse_fasta(open(e, 'U')) for e in opts.centroid_fps]
    singleton_seqs = \
        [parse_fasta(open(e, 'U')) for e in opts.singleton_fps]
    fasta_seqs = \
        [parse_fasta(open(e, 'U')) for e in opts.fasta_fps]
    denoiser_map_fs = \
        [open(e, 'U') for e in opts.denoiser_map_fps]
    output_fasta_fp = opts.output_fasta_fp

    output_f = open(opts.output_fasta_fp, 'w')
    for s in inflate_denoiser_output(chain.from_iterable(centroid_seqs),
                                     chain.from_iterable(singleton_seqs),
                                     chain.from_iterable(denoiser_map_fs),
                                     chain.from_iterable(fasta_seqs)):
        output_f.write('>%s\n%s\n' % s)
    output_f.close()

Example #3

File: inflate_denoiser_output.py Project: Springbudder/qiime

def main():
    option_parser, opts, args =\
        parse_command_line_parameters(**script_info)

    centroid_seqs = \
        [parse_fasta(open(e, 'U')) for e in opts.centroid_fps]
    singleton_seqs = \
        [parse_fasta(open(e, 'U')) for e in opts.singleton_fps]
    fasta_seqs = \
        [parse_fasta(open(e, 'U')) for e in opts.fasta_fps]
    denoiser_map_fs = \
        [open(e, 'U') for e in opts.denoiser_map_fps]
    output_fasta_fp = opts.output_fasta_fp

    output_f = open(opts.output_fasta_fp, 'w')
    for s in inflate_denoiser_output(
            chain.from_iterable(centroid_seqs),
            chain.from_iterable(singleton_seqs),
            chain.from_iterable(denoiser_map_fs),
            chain.from_iterable(fasta_seqs)):
        output_f.write('>%s\n%s\n' % s)
    output_f.close()