def test_add_qiime_labels_valid_data(self): """ Tests overall script functionality """ # With valid data should not raise any errors mapping_data = [ '#SampleID BarcodeSequence LinkerPrimerSequence InputFileNames Description', 'Sample1 AAAA ACTG %s S1' % basename(self.fasta1_fp), 'Sample2 TTTT ACTG %s S2' % basename(self.fasta2_fp), 'Sample3 CCCC ACTG %s S3' % basename(self.fasta3_fp) ] filename_column = "InputFileNames" add_qiime_labels(mapping_data, self.input_dir, filename_column, self.output_dir) output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U") output_lines = [line.strip() for line in output_fp] expected_output_lines = [ '>Sample1_0 label1 XXX', 'ACAGATTACGA', '>Sample1_1 label2 YYY', 'ACATAAAATAGCCGGAG', '>Sample2_2 label3 ZZZ', 'AACGYAACGAGA', '>Sample2_3 label4', 'ACAGAGAGAGGGGAGA', '>Sample3_4 label5 ;LKJ', 'ACAGGGATTTTTAT' ] self.assertEqual(output_lines, expected_output_lines)
def test_add_qiime_labels_valid_data(self): """ Tests overall script functionality """ # With valid data should not raise any errors mapping_data = [ '#SampleID BarcodeSequence LinkerPrimerSequence InputFileNames Description', 'Sample1 AAAA ACTG %s S1' % basename(self.fasta1_fp), 'Sample2 TTTT ACTG %s S2' % basename(self.fasta2_fp), 'Sample3 CCCC ACTG %s S3' % basename(self.fasta3_fp) ] filename_column = "InputFileNames" add_qiime_labels(mapping_data, self.input_dir, filename_column, self.output_dir) output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U") output_lines = [line.strip() for line in output_fp] expected_output_lines = ['>Sample1_0 label1 XXX', 'ACAGATTACGA', '>Sample1_1 label2 YYY', 'ACATAAAATAGCCGGAG', '>Sample2_2 label3 ZZZ', 'AACGYAACGAGA', '>Sample2_3 label4', 'ACAGAGAGAGGGGAGA', '>Sample3_4 label5 ;LKJ', 'ACAGGGATTTTTAT'] self.assertEqual(output_lines, expected_output_lines)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) mapping_fp = opts.mapping_fp fasta_dir = opts.fasta_dir output_dir = opts.output_dir count_start = int(opts.count_start) filename_column = opts.filename_column # Check input filepaths try: test_mapping_f = open(mapping_fp, "U") except IOError: raise IOError,("Cannot open mapping filepath "+\ "%s, please check filepath and permissions." % mapping_fp) if not isdir(fasta_dir): raise IOError, ("Specified fasta dir " + "%s, does not exist" % fasta_dir) # Create output directory, check path/access to mapping file create_dir(output_dir) add_qiime_labels(open(mapping_fp, "U"), fasta_dir, filename_column, output_dir, count_start)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) mapping_fp = opts.mapping_fp fasta_dir = opts.fasta_dir output_dir = opts.output_dir count_start = int(opts.count_start) filename_column = opts.filename_column # Check input filepaths try: test_mapping_f = open(mapping_fp, "U") except IOError: raise IOError,("Cannot open mapping filepath "+\ "%s, please check filepath and permissions." % mapping_fp) if not isdir(fasta_dir): raise IOError,("Specified fasta dir "+ "%s, does not exist" % fasta_dir) # Create output directory, check path/access to mapping file create_dir(output_dir) add_qiime_labels(open(mapping_fp, "U"), fasta_dir, filename_column, output_dir, count_start)
def test_add_qiime_labels_valid_data(self): """ Tests overall script functionality """ # With valid data should not raise any errors mapping_data = ['Sample1\t%s' % basename(self.fasta1_fp), 'Sample2\t%s' % basename(self.fasta2_fp), 'Sample3\t%s' % basename(self.fasta3_fp) ] add_qiime_labels(mapping_data, self.input_dir, self.output_dir) output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U") output_lines = [line.strip() for line in output_fp] expected_output_lines = ['>Sample2_0 label3 ZZZ', 'AACGYAACGAGA', '>Sample2_1 label4', 'ACAGAGAGAGGGGAGA', '>Sample3_2 label5 ;LKJ', 'ACAGGGATTTTTAT', '>Sample1_3 label1 XXX', 'ACAGATTACGA', '>Sample1_4 label2 YYY', 'ACATAAAATAGCCGGAG'] self.assertEqual(output_lines, expected_output_lines)
def test_add_qiime_labels_valid_data(self): """ Tests overall script functionality """ # With valid data should not raise any errors mapping_data = [ 'Sample1\t%s' % basename(self.fasta1_fp), 'Sample2\t%s' % basename(self.fasta2_fp), 'Sample3\t%s' % basename(self.fasta3_fp) ] add_qiime_labels(mapping_data, self.input_dir, self.output_dir) output_fp = open(join(self.output_dir, "combined_seqs.fna"), "U") output_lines = [line.strip() for line in output_fp] expected_output_lines = [ '>Sample2_0 label3 ZZZ', 'AACGYAACGAGA', '>Sample2_1 label4', 'ACAGAGAGAGGGGAGA', '>Sample3_2 label5 ;LKJ', 'ACAGGGATTTTTAT', '>Sample1_3 label1 XXX', 'ACAGATTACGA', '>Sample1_4 label2 YYY', 'ACATAAAATAGCCGGAG' ] self.assertEqual(output_lines, expected_output_lines)