Ejemplos de GenomeStatus.write_to_fasta_file en Python

Ejemplo n.º 1

Archivo: find_duplicates.py Proyecto: TGenNorth/NASP

def main():
    from nasp.nasp_objects import GenomeStatus

    commandline_args = _parse_args()
    run_nucmer_on_reference(commandline_args.nucmerpath, commandline_args.reference)
    dups_data = GenomeStatus()
    parse_delta_file("reference.delta", dups_data)
    dups_data.write_to_fasta_file("duplicates.txt")

Ejemplo n.º 2

Archivo: find_duplicates.py Proyecto: wangdi2014/NASP

def main():
    from nasp.nasp_objects import GenomeStatus

    commandline_args = _parse_args()
    run_nucmer_on_reference(commandline_args.nucmerpath,
                            commandline_args.reference)
    dups_data = GenomeStatus()
    parse_delta_file("reference.delta", dups_data)
    dups_data.write_to_fasta_file("duplicates.txt")

Ejemplo n.º 3

Archivo: find_duplicates_test.py Proyecto: TGenNorth/NASP

    def test_parse_delta_file(self):
        import itertools
        from nasp.nasp_objects import GenomeStatus
        from tests import testdata
        from tempfile import NamedTemporaryFile

        dups_data = GenomeStatus()
        find_duplicates.parse_delta_file(testdata.REFERENCE_DELTA, dups_data)
        with NamedTemporaryFile() as tmpfile:
            dups_data.write_to_fasta_file(tmpfile.name)
            with  open(testdata.REFERENCE_DUPS) as expected, open(tmpfile.name) as observed:
                for expect, observe in itertools.zip_longest(expected, observed):
                    self.assertEqual(expect, observe)

Ejemplo n.º 4

    def test_parse_delta_file(self):
        import itertools
        from nasp.nasp_objects import GenomeStatus
        from tests import testdata
        from tempfile import NamedTemporaryFile

        dups_data = GenomeStatus()
        find_duplicates.parse_delta_file(testdata.REFERENCE_DELTA, dups_data)
        with NamedTemporaryFile() as tmpfile:
            dups_data.write_to_fasta_file(tmpfile.name)
            with open(testdata.REFERENCE_DUPS) as expected, open(
                    tmpfile.name) as observed:
                for expect, observe in itertools.zip_longest(
                        expected, observed):
                    self.assertEqual(expect, observe)