Esempi in Python per get_otu_ids_from_taxonomy_f

Esempio n. 1

File: filter_taxa_from_otu_table.py Progetto: ElDeveloper/qiime

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

    output_table_fp = opts.output_otu_table_fp
    metadata_field = opts.metadata_field
    positive_taxa = opts.positive_taxa
    negative_taxa = opts.negative_taxa

    input_table = load_table(opts.input_otu_table_fp)

    if positive_taxa is not None:
        positive_taxa = positive_taxa.split(',')
    else:
        positive_taxa = None

    if negative_taxa is not None:
        negative_taxa = negative_taxa.split(',')
    else:
        negative_taxa = None

    filter_fn = get_otu_ids_from_taxonomy_f(positive_taxa, negative_taxa,
                                            metadata_field)
    input_table.filter(filter_fn, axis='observation')

    try:
        write_biom_table(input_table, output_table_fp)
    except EmptyBIOMTableError:
        option_parser.error(
            "Filtering resulted in an empty BIOM table. "
            "This indicates that no OTUs remained after filtering.")

Esempio n. 2

File: filter_taxa_from_otu_table.py Progetto: wilkox/qiime

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

    input_table = parse_biom_table(open(opts.input_otu_table_fp, 'U'))
    output_table_f = open(opts.output_otu_table_fp, 'w')
    metadata_field = opts.metadata_field
    positive_taxa = opts.positive_taxa
    negative_taxa = opts.negative_taxa

    if positive_taxa is not None:
        positive_taxa = positive_taxa.split(',')
    else:
        positive_taxa = None

    if negative_taxa is not None:
        negative_taxa = negative_taxa.split(',')
    else:
        negative_taxa = None

    filter_fn = get_otu_ids_from_taxonomy_f(
        positive_taxa,
        negative_taxa,
        metadata_field)
    output_table = input_table.filterObservations(filter_fn)
    output_table_f.write(format_biom_table(output_table))
    output_table_f.close()

Esempio n. 3

File: filter_taxa_from_otu_table.py Progetto: AhmedAbdelfattah/qiime

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

    output_table_fp = opts.output_otu_table_fp
    metadata_field = opts.metadata_field
    positive_taxa = opts.positive_taxa
    negative_taxa = opts.negative_taxa

    input_table = load_table(opts.input_otu_table_fp)

    if positive_taxa is not None:
        positive_taxa = positive_taxa.split(',')
    else:
        positive_taxa = None

    if negative_taxa is not None:
        negative_taxa = negative_taxa.split(',')
    else:
        negative_taxa = None

    filter_fn = get_otu_ids_from_taxonomy_f(positive_taxa, negative_taxa,
                                            metadata_field)
    input_table.filter(filter_fn, axis='observation')

    write_biom_table(input_table, output_table_fp)

Esempio n. 4

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

    output_table_fp = opts.output_otu_table_fp
    metadata_field = opts.metadata_field
    positive_taxa = opts.positive_taxa
    negative_taxa = opts.negative_taxa

    input_table = load_table(opts.input_otu_table_fp)

    if positive_taxa is not None:
        positive_taxa = positive_taxa.split(',')
    else:
        positive_taxa = None

    if negative_taxa is not None:
        negative_taxa = negative_taxa.split(',')
    else:
        negative_taxa = None

    filter_fn = get_otu_ids_from_taxonomy_f(positive_taxa, negative_taxa,
                                            metadata_field)
    input_table.filter(filter_fn, axis='observation')

    try:
        write_biom_table(input_table, output_table_fp)
    except EmptyBIOMTableError:
        option_parser.error(
            "Filtering resulted in an empty BIOM table. "
            "This indicates that no OTUs remained after filtering.")

Esempio n. 5

File: filter_taxa_from_otu_table.py Progetto: shiffer1/qiime

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

    output_table_fp = opts.output_otu_table_fp
    metadata_field = opts.metadata_field
    positive_taxa = opts.positive_taxa
    negative_taxa = opts.negative_taxa

    input_table = load_table(opts.input_otu_table_fp)

    if positive_taxa is not None:
        positive_taxa = positive_taxa.split(',')
    else:
        positive_taxa = None

    if negative_taxa is not None:
        negative_taxa = negative_taxa.split(',')
    else:
        negative_taxa = None

    filter_fn = get_otu_ids_from_taxonomy_f(positive_taxa, negative_taxa,
                                            metadata_field)
    input_table.filter(filter_fn, axis='observation')

    write_biom_table(input_table, output_table_fp)