Python Genome.write_to_fasta_file примеры использования

Пример #1

Файл: convert_external_genome_test.py Проект: TGenNorth/NASP

    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())

Пример #2

    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())

Пример #3

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)

Пример #4

Файл: format_fasta.py Проект: TGenNorth/NASP

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)