def test_parse_delta_file(self): from tests import testdata from tempfile import NamedTemporaryFile from nasp.nasp_objects import Genome franken_genome = Genome() external_genome = Genome() external_genome.import_fasta_file(testdata.REFERENCE_FASTA) convert_external_genome.parse_delta_file(testdata.REFERENCE_DELTA, franken_genome, external_genome) with NamedTemporaryFile() as tmpfile: franken_genome.write_to_fasta_file(tmpfile.name) with open(testdata.REFERENCE_FASTA) as expected, open(tmpfile.name) as actual: self.assertEqual(expected.readlines(), actual.readlines())
def test_parse_delta_file(self): from tests import testdata from tempfile import NamedTemporaryFile from nasp.nasp_objects import Genome franken_genome = Genome() external_genome = Genome() external_genome.import_fasta_file(testdata.REFERENCE_FASTA) convert_external_genome.parse_delta_file(testdata.REFERENCE_DELTA, franken_genome, external_genome) with NamedTemporaryFile() as tmpfile: franken_genome.write_to_fasta_file(tmpfile.name) with open(testdata.REFERENCE_FASTA) as expected, open( tmpfile.name) as actual: self.assertEqual(expected.readlines(), actual.readlines())
def format_fasta(inputfasta, outputfasta): from nasp.nasp_objects import Genome fasta_data = Genome() fasta_data.import_fasta_file(inputfasta) fasta_data.write_to_fasta_file(outputfasta)