def main():
import subprocess
from nasp.nasp_objects import Genome, GenomeMeta
commandline_args = _parse_args()
external_nickname = commandline_args.name if commandline_args.name else GenomeMeta.generate_nickname_from_filename(
commandline_args.external)
#external_genome = Genome()
#external_genome.import_fasta_file(commandline_args.external)
generate_delta_file(commandline_args.nucmerpath,
commandline_args.nucmerargs,
commandline_args.deltafilterpath,
commandline_args.deltafilterargs, external_nickname,
commandline_args.reference, commandline_args.external)
#franken_genome = Genome()
#parse_delta_file(( external_nickname + ".filtered.delta" ), franken_genome, external_genome)
#franken_genome.write_to_fasta_file(external_nickname + ".frankenfasta", "franken::")
import pkg_resources
nasptool_path = pkg_resources.resource_filename('nasp',
'nasptool_linux_64')
with open(external_nickname + ".frankenfasta", 'w') as handle:
return_code = subprocess.call([
nasptool_path, "frankenfasta",
external_nickname + ".filtered.delta"
],
stdout=handle)
def main():
import subprocess
from nasp.nasp_objects import Genome, GenomeMeta
commandline_args = _parse_args()
external_nickname = commandline_args.name if commandline_args.name else GenomeMeta.generate_nickname_from_filename(
commandline_args.external)
#external_genome = Genome()
#external_genome.import_fasta_file(commandline_args.external)
generate_delta_file(commandline_args.nucmerpath, commandline_args.nucmerargs, commandline_args.deltafilterpath,
commandline_args.deltafilterargs, external_nickname, commandline_args.reference,
commandline_args.external)
#franken_genome = Genome()
#parse_delta_file(( external_nickname + ".filtered.delta" ), franken_genome, external_genome)
#franken_genome.write_to_fasta_file(external_nickname + ".frankenfasta", "franken::")
import pkg_resources
nasptool_path = pkg_resources.resource_filename('nasp', 'nasptool_linux_64')
with open(external_nickname + ".frankenfasta", 'w') as handle:
return_code = subprocess.call([nasptool_path, "frankenfasta", external_nickname + ".filtered.delta"], stdout=handle)
def setUp(self):
self.genome = GenomeMeta()
class GenomeMetaTestCase(unittest.TestCase):
def setUp(self):
self.genome = GenomeMeta()
# TODO: Should the side effect of setting an undefined nickname be tested?
def test_set_file_path(self):
expected = "foo"
self.genome.set_file_path(expected)
self.assertEqual(expected, self.genome.file_path())
def test_set_file_type(self):
expected = "foo"
self.genome.set_file_type(expected)
self.assertEqual(expected, self.genome.file_type())
def test_set_nickname(self):
expected = "foo"
self.genome.set_nickname(expected)
self.assertEqual(expected, self.genome.nickname())
@unittest.skip("Not Implemented")
def test_add_generators(self):
pass
def test_file_path(self):
expected = "foo"
self.assertIsNone(self.genome.file_path())
self.genome.set_file_path(expected)
self.assertEqual(expected, self.genome.file_path())
def test_file_type(self):
expected = "foo"
self.assertIsNone(self.genome.file_type())
self.genome.set_file_type(expected)
self.assertEqual(expected, self.genome.file_type())
def test_nickname(self):
expected = "foo"
self.assertIsNone(self.genome.nickname())
self.genome.set_nickname(expected)
self.assertEqual(expected, self.genome.nickname())
pass
def test_identifier(self):
generators = ["bar", "baz", "quox"]
nickname = "foo"
self.assertIsNone(self.genome.identifier())
self.genome.set_nickname(nickname)
self.assertEqual(nickname, self.genome.identifier())
self.genome.add_generators(generators)
self.assertEqual(nickname + "::" + ",".join(generators), self.genome.identifier())
def test_generate_nickname_from_filename(self):
expected = "foo"
paths = ["", "/", "/bar/baz/quox/" "bar/baz/quox/"]
extensions = [".fRaNkEnFaStA", ".FaStA", ".fAs", ".VcF"]
for extension in extensions:
filename = expected + extension
self.assertEqual(expected, self.genome.generate_nickname_from_filename(filename))
for path in paths:
filename = path + expected + ".vcf"
self.assertEqual(expected, self.genome.generate_nickname_from_filename(filename))
@unittest.skip("Duplicate of Genome.reverse_complement")
def test_reverse_complement(dna_string):
pass
def setUp(self):
self.genome = GenomeMeta()
class GenomeMetaTestCase(unittest.TestCase):
def setUp(self):
self.genome = GenomeMeta()
# TODO: Should the side effect of setting an undefined nickname be tested?
def test_set_file_path(self):
expected = 'foo'
self.genome.set_file_path(expected)
self.assertEqual(expected, self.genome.file_path())
def test_set_file_type(self):
expected = 'foo'
self.genome.set_file_type(expected)
self.assertEqual(expected, self.genome.file_type())
def test_set_nickname(self):
expected = 'foo'
self.genome.set_nickname(expected)
self.assertEqual(expected, self.genome.nickname())
@unittest.skip("Not Implemented")
def test_add_generators(self):
pass
def test_file_path(self):
expected = 'foo'
self.assertIsNone(self.genome.file_path())
self.genome.set_file_path(expected)
self.assertEqual(expected, self.genome.file_path())
def test_file_type(self):
expected = 'foo'
self.assertIsNone(self.genome.file_type())
self.genome.set_file_type(expected)
self.assertEqual(expected, self.genome.file_type())
def test_nickname(self):
expected = 'foo'
self.assertIsNone(self.genome.nickname())
self.genome.set_nickname(expected)
self.assertEqual(expected, self.genome.nickname())
pass
def test_identifier(self):
generators = ['bar', 'baz', 'quox']
nickname = 'foo'
self.assertIsNone(self.genome.identifier())
self.genome.set_nickname(nickname)
self.assertEqual(nickname, self.genome.identifier())
self.genome.add_generators(generators)
self.assertEqual(nickname + '::' + ','.join(generators),
self.genome.identifier())
def test_generate_nickname_from_filename(self):
expected = 'foo'
paths = ['', '/', '/bar/baz/quox/' 'bar/baz/quox/']
extensions = ['.fRaNkEnFaStA', '.FaStA', '.fAs', '.VcF']
for extension in extensions:
filename = expected + extension
self.assertEqual(
expected,
self.genome.generate_nickname_from_filename(filename))
for path in paths:
filename = path + expected + '.vcf'
self.assertEqual(
expected,
self.genome.generate_nickname_from_filename(filename))
@unittest.skip("Duplicate of Genome.reverse_complement")
def test_reverse_complement(dna_string):
pass
