def setUp(self): self.qiime_config = load_qiime_config() self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/' #Temporary input file fd, self.tmp_otu_fp = mkstemp(dir=self.tmp_dir, prefix='R_test_otu_table_', suffix='.biom') close(fd) seq_file = open(self.tmp_otu_fp, 'w') seq_file.write(test_otu_table) seq_file.close() self.tmp_otu_fp_out_CSS = '%s/R_test_otu_table_out_CSS.biom' % (str( self.tmp_dir)) self.tmp_otu_fp_out_DESeq = '%s/R_test_otu_table_out_DESeq.biom' % ( str(self.tmp_dir)) self.files_to_remove = \ [self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, self.tmp_otu_fp_out_DESeq] normalize_CSS(self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, output_CSS_statistics=False) normalize_DESeq2(self.tmp_otu_fp, self.tmp_otu_fp_out_DESeq, DESeq_negatives_to_zero=False)
def test_normalize_table_CSS(self): normalize_CSS(self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, output_CSS_statistics=False) input_table = load_table(self.tmp_otu_fp) output_table = load_table(self.tmp_otu_fp_out_CSS) self.compare_tables(input_table, output_table)
def setUp(self): self.qiime_config = load_qiime_config() self.tmp_dir = self.qiime_config['temp_dir'] or '/tmp/' #Temporary input file fd, self.tmp_otu_fp = mkstemp(dir= self.tmp_dir, prefix='R_test_otu_table_', suffix='.biom') close(fd) seq_file = open(self.tmp_otu_fp, 'w') seq_file.write(test_otu_table) seq_file.close() self.tmp_otu_fp_out_CSS = '%s/R_test_otu_table_out_CSS.biom' % (str(self.tmp_dir)) self.tmp_otu_fp_out_DESeq = '%s/R_test_otu_table_out_DESeq.biom' % (str(self.tmp_dir)) self.files_to_remove = \ [self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, self.tmp_otu_fp_out_DESeq] normalize_CSS(self.tmp_otu_fp, self.tmp_otu_fp_out_CSS, output_CSS_statistics=False) normalize_DESeq2(self.tmp_otu_fp, self.tmp_otu_fp_out_DESeq, DESeq_negatives_to_zero=False)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) input_path = opts.input_path out_path = opts.out_path output_CSS_statistics = opts.output_CSS_statistics DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero algorithm = opts.algorithm list_algorithms = opts.list_algorithms if list_algorithms: print 'Available normalization algorithms are:\n%s' % ', '.join( algorithm_list()) else: almost_required_options = ['input_path', 'out_path'] for option in almost_required_options: if getattr(opts, option) is None: option_parser.error('Required option --%s omitted.' % option) if algorithm == 'CSS': if os.path.isdir(input_path): multiple_file_normalize_CSS(input_path, out_path, output_CSS_statistics) elif os.path.isfile(input_path): normalize_CSS(input_path, out_path, output_CSS_statistics) else: # it shouldn't be possible to get here option_parser.error("Unknown input type: %s" % input_path) elif algorithm == 'DESeq2': if os.path.isdir(input_path): multiple_file_normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero) elif os.path.isfile(input_path): normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero) else: # it shouldn't be possible to get here option_parser.error("Unknown input type: %s" % input_path) else: # it shouldn't be possible to get here option_parser.error("Unknown normalization algorithm: %s" % algorithm)
def main(): option_parser, opts, args = parse_command_line_parameters(**script_info) input_path = opts.input_path out_path = opts.out_path output_CSS_statistics = opts.output_CSS_statistics DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero algorithm = opts.algorithm list_algorithms = opts.list_algorithms if list_algorithms: print 'Available normalization algorithms are:\n%s' % ', '.join(algorithm_list()) else: almost_required_options = ['input_path', 'out_path'] for option in almost_required_options: if getattr(opts, option) is None: option_parser.error('Required option --%s omitted.' % option) if algorithm == 'CSS': if os.path.isdir(input_path): multiple_file_normalize_CSS(input_path, out_path, output_CSS_statistics) elif os.path.isfile(input_path): normalize_CSS(input_path, out_path, output_CSS_statistics) else: # it shouldn't be possible to get here option_parser.error("Unknown input type: %s" % input_path) elif algorithm == 'DESeq2': if os.path.isdir(input_path): multiple_file_normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero) elif os.path.isfile(input_path): normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero) else: # it shouldn't be possible to get here option_parser.error("Unknown input type: %s" % input_path) else: # it shouldn't be possible to get here option_parser.error("Unknown normalization algorithm: %s" % algorithm)