Exemplos de process_extract_samples em Python

Exemplo n.º 1

Arquivo: test_filter_otus_by_sample.py Projeto: Ecogenomics/FrankenQIIME

    def test_process_extract_samples(self):
        """process_extract_samples: parses the cmd line and determines which
samples should be removed"""

        self.sample_to_extract='SampleA,SampleB'
        exp1={'0':'SampleA','1':'SampleB'}

        obs1=process_extract_samples(self.sample_to_extract)

        self.assertEqual(obs1,exp1)

Exemplo n.º 2

Arquivo: test_filter_otus_by_sample.py Projeto: rob-knight/qiime

    def test_process_extract_samples(self):
        """process_extract_samples: parses the cmd line and determines which
samples should be removed"""

        self.sample_to_extract = "SampleA,SampleB"
        exp1 = {"0": "SampleA", "1": "SampleB"}

        obs1 = process_extract_samples(self.sample_to_extract)

        self.assertEqual(obs1, exp1)

Exemplo n.º 3

Arquivo: filter_otus_by_sample.py Projeto: AhmedAbdelfattah/qiime

def main():
    """opens files as necessary based on prefs"""
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    data = {}

    fasta_file = opts.input_fasta_fp

    # load the input alignment
    data['aln'] = SequenceCollection.from_fasta_records(
        parse_fasta(open(fasta_file)), DNA)

    # Load the otu file
    otu_path = opts.otu_map_fp
    otu_f = open(otu_path, 'U')
    otus = fields_to_dict(otu_f)
    otu_f.close()

    data['otus'] = otus
    # Determine which which samples to extract from representative seqs
    # and from otus file
    if opts.samples_to_extract:
        prefs = process_extract_samples(opts.samples_to_extract)

    filepath = opts.input_fasta_fp
    filename = filepath.strip().split('/')[-1]
    filename = filename.split('.')[0]

    if opts.output_dir:
        if os.path.exists(opts.output_dir):
            dir_path = opts.output_dir
        else:
            try:
                os.mkdir(opts.output_dir)
                dir_path = opts.output_dir
            except OSError:
                pass
    else:
        dir_path = './'

    try:
        action = filter_samples
    except NameError:
        action = None
    # Place this outside try/except so we don't mask NameError in action
    if action:
        action(prefs, data, dir_path, filename)

Exemplo n.º 4

Arquivo: filter_otus_by_sample.py Projeto: davidvilanova/qiime

def main():
    """opens files as necessary based on prefs"""
    option_parser, opts, args = parse_command_line_parameters(**script_info)

    data = {}

    fasta_file = opts.input_fasta_fp

    # load the input alignment
    data['aln'] = SequenceCollection.from_fasta_records(
        parse_fasta(open(fasta_file)), DNA)

    # Load the otu file
    otu_path = opts.otu_map_fp
    otu_f = open(otu_path, 'U')
    otus = fields_to_dict(otu_f)
    otu_f.close()

    data['otus'] = otus
    # Determine which which samples to extract from representative seqs
    # and from otus file
    if opts.samples_to_extract:
        prefs = process_extract_samples(opts.samples_to_extract)

    filepath = opts.input_fasta_fp
    filename = filepath.strip().split('/')[-1]
    filename = filename.split('.')[0]

    if opts.output_dir:
        if os.path.exists(opts.output_dir):
            dir_path = opts.output_dir
        else:
            try:
                os.mkdir(opts.output_dir)
                dir_path = opts.output_dir
            except OSError:
                pass
    else:
        dir_path = './'

    try:
        action = filter_samples
    except NameError:
        action = None
    # Place this outside try/except so we don't mask NameError in action
    if action:
        action(prefs, data, dir_path, filename)