def test_fasta__from_file__compressed_bz2(): expected = [ FASTA("This_is_BZ_FASTA!", None, "CGTNA"), FASTA("This_is_ALSO_BZ_FASTA!", None, "ACGTN") ] results = list(FASTA.from_file("tests/data/fasta_file.fasta.bz2")) assert_equal(results, expected)
def __init__(self, options, filename): genome = list(FASTA.from_file(filename)) assert len(genome) == 1, len(genome) self._genome = genome[0].sequence.upper() self._sequence = None self._positions = None self._annotations = None self._mutate(options)
def _setup(self, _config, temp): self._update_ctl_file(source = self._control_file, destination = os.path.join(temp, "template.ctl")) os.symlink(os.path.abspath(self._trees_file), os.path.join(temp, "template.trees")) with open(os.path.join(temp, "template.seqs"), "w") as handle: for record in FASTA.from_file(self._sequence_file): if record.name not in self._exclude_groups: name = record.name sequence = record.sequence.upper() handle.write("%s\n" % (FASTA(name, None, sequence),))
def test_fasta__from_file__compressed_bz2(): expected = [FASTA("This_is_BZ_FASTA!", None, "CGTNA"), FASTA("This_is_ALSO_BZ_FASTA!", None, "ACGTN")] results = list(FASTA.from_file("tests/data/fasta_file.fasta.bz2")) assert_equal(results, expected)