def test_truncate_fasta_qual(self): """ Test for overall module functionality """ base_pos = 80 output_dir = '/tmp/truncate_fasta_qual_test/' create_dir(output_dir) truncate_fasta_qual(self.fasta_fp, self.qual_fp, output_dir, base_pos) actual_trunc_fasta_fp = output_dir +\ basename(self.fasta_fp).replace(".fasta", "_filtered.fasta") actual_trunc_fasta_fp = open(actual_trunc_fasta_fp, "U") actual_trunc_fasta = [line.strip() for line in actual_trunc_fasta_fp] self.assertEqual(actual_trunc_fasta, expected_fasta_seqs) actual_trunc_qual_fp = output_dir +\ basename(self.qual_fp).replace(".qual", "_filtered.qual") actual_trunc_qual_fp = open(actual_trunc_qual_fp, "U") actual_trunc_qual = [line.strip() for line in actual_trunc_qual_fp] self.assertEqual(actual_trunc_qual, expected_qual_scores)
def main(): option_parser, opts, args =\ parse_command_line_parameters(**script_info) fasta_fp = opts.fasta_fp qual_fp = opts.qual_fp output_dir = opts.output_dir base_pos = int(opts.base_pos) create_dir(output_dir) truncate_fasta_qual(fasta_fp, qual_fp, output_dir, base_pos)