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")
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")
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)
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)
class GenomeStatusTestCase(unittest.TestCase):
def setUp(self):
self.genome = GenomeStatus()
def test_add_contig(self):
expected = ['foo']
self.genome.add_contig(expected[0])
self.assertEqual(expected, self.genome.get_contigs())
def test_add_contig_with_contig_name_none_raises_invalidcontigname(self):
with self.assertRaises(InvalidContigName):
self.genome.add_contig(None)
def test_add_contig_with_contig_name_empty_raises_invalidcontigname(self):
with self.assertRaises(InvalidContigName):
self.genome.add_contig("")
def test_add_contig_with_duplicate_contig_name_raises_invalidcontigname(
self):
with self.assertRaises(InvalidContigName):
self.genome.add_contig('duplicate')
self.genome.add_contig('duplicate')
def test_set_current_contig_with_contig_name_none(self):
self.assertIsNone(self.genome.set_current_contig(None))
# Special case: getter behavior when argument is None
def test_set_current_contig_with_contig_name_none_returns_current_config(
self):
expected = 'foo'
self.genome.add_contig(expected)
self.assertEqual(expected, self.genome.set_current_contig(None))
def test_set_current_contig_with_contig_name_invalid_and_create_contig_false_raises_invalidcontigname(
self):
with self.assertRaises(InvalidContigName):
self.genome.set_current_contig('invalid_contig_name', False)
def test_set_current_contig_with_contig_name_valid_and_create_contig_false(
self):
expected = 'foo'
self.genome.add_contig(expected)
self.genome.add_contig('bar')
self.assertEqual(expected,
self.genome.set_current_contig(expected, False))
def test_get_contigs_empty(self):
self.assertListEqual([], self.genome.get_contigs())
def test_get_contigs(self):
expected = ['a', 'b', 'c']
# Reverse the list to verify the returned list is sorted
for contig in reversed(expected):
self.genome.add_contig(contig)
self.assertListEqual(expected, self.genome.get_contigs())
def test_append_contig_with_single_nucleotide(self):
expected = ['A']
contig_name = 'foo'
self.genome.append_contig(expected[0], contig_name)
self.assertListEqual(expected,
self.genome.get_value(1, -1, contig_name))
def test_append_contig_with_list(self):
expected = ['A', 'C', 'G', 'T', 'U']
contig_name = 'foo'
self.genome.append_contig(expected, contig_name)
self.assertListEqual(expected,
self.genome.get_value(1, -1, contig_name))
# TODO: make placeholder an optional final parameter
def test_extend_contig(self):
data = ['A', 'C', 'G', 'T', 'U']
placeholder = '@'
contig_name = 'foo'
expected_length = len(data) + 5
expected_content = list(data)
expected_content.extend([placeholder] * 5)
self.genome.append_contig(data, contig_name)
self.genome.extend_contig(expected_length, placeholder, contig_name)
# It allocated the additional space
self.assertEqual(expected_length,
self.genome.get_contig_length(contig_name))
# It filled the allocated space after the data with the placeholder
self.assertListEqual(expected_content,
self.genome.get_value(1, -1, contig_name))
def test_extend_contig_when_empty(self):
expected = 42
placeholder = '@'
contig_name = 'foo'
self.genome.add_contig(contig_name)
self.genome.extend_contig(expected, placeholder, contig_name)
# It allocated the additional space
self.assertEqual(expected, self.genome.get_contig_length(contig_name))
# It filled the undefined areas with the placeholder
self.assertListEqual([placeholder] * expected,
self.genome.get_value(1, -1, contig_name))
def test_extend_contig_does_not_shrink_contig(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
expected = len(data)
placeholder = '@'
self.genome.append_contig(data, contig_name)
self.genome.extend_contig(0, placeholder, contig_name)
# It did not shrink the contig
self.assertEqual(expected, self.genome.get_contig_length(contig_name))
# It did not overwrite the existing data with a placeholder
self.assertListEqual(data, self.genome.get_value(1, -1, contig_name))
def test_set_value(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.set_value(data, 1, contig_name=contig_name)
# Given a list, it should set the range of elements beginning with the start position
self.assertListEqual(data, self.genome.get_value(1, -1, contig_name))
self.genome.set_value('A', 3, contig_name=contig_name)
data[2] = 'A'
# Given a character, it should set the element at the start position
self.assertListEqual(data, self.genome.get_value(1, -1, contig_name))
# TODO: Should it instead raise an exception?
def test_set_value_out_of_bounds(self):
contig_name = 'foo'
placeholder = '!'
expected = [placeholder] * 4
expected.append('A')
# It should fill the interim elements with the placeholder when setting an out of bounds element
self.genome.set_value('A',
5,
missing_range_filler="!",
contig_name=contig_name)
self.assertEqual(expected, self.genome.get_value(1, -1, contig_name))
# FIXME: get_value returns 3 data types - list, string, None
def test_get_value_with_first_position(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertEqual('A', self.genome.get_value(1,
contig_name=contig_name))
def test_get_value_with_last_position(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertEqual(data, self.genome.get_value(1, -1, contig_name))
def test_get_value_empty(self):
contig_name = 'foo'
self.genome.add_contig(contig_name)
self.assertEqual([], self.genome.get_value(1, contig_name=contig_name))
def test_get_value_with_contig_name_invalid(self):
self.assertEqual([], self.genome.get_value(1, contig_name='invalid'))
def test_get_value_with_invalid_position_raises_indexerror(self):
with self.assertRaises(IndexError):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.genome.get_value(0, contig_name=contig_name)
def test_get_value_range_of_one(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertListEqual(['C'], self.genome.get_value(2, 2, contig_name))
def test_get_value_reversed_position_values(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertEqual([],
self.genome.get_value(2, 1, contig_name=contig_name))
# TODO: Could this hide index errors?
def test_get_value_outside_range(self):
contig_name = 'foo'
expected = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(expected, contig_name)
self.assertListEqual(
expected, self.genome.get_value(1, 10, contig_name=contig_name))
# TODO: Is there a conflict if there are different placeholders?
# Example: contig_extend fills allocated region with placeholder A,
# but get_value retrieves an even larger region filling it with placeholder B
# the result might be: [d,a,t,a,A,A,A,A,B,B,B,B]
def test_get_value_outside_range_with_filler(self):
contig_name = 'foo'
placeholder = '@'
data = ['A', 'C', 'G', 'T', 'U']
expected = list(data)
expected.extend([placeholder] * 5)
self.genome.append_contig(data, contig_name)
# It should fill out of bounds region with the placeholder
self.assertListEqual(
expected,
self.genome.get_value(1,
10,
contig_name=contig_name,
placeholder=placeholder))
def test_get_contig_length(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.add_contig(contig_name)
self.genome.append_contig(data, contig_name)
self.assertEqual(len(data), self.genome.get_contig_length(contig_name))
def test_get_contig_length_when_empty(self):
contig_name = 'foo'
self.genome.add_contig(contig_name)
self.assertEqual(0, self.genome.get_contig_length(contig_name))
def test_get_contig_length_with_contig_name_invalid(self):
self.assertEqual(0, self.genome.get_contig_length('invalid'))
def test_get_contig_length_with_contig_name_none(self):
# FIXME: test fails without self.genome.add_contig(None)
self.assertEqual(0, self.genome.get_contig_length(None))
def test_send_to_fasta_handle(self):
# contigs are sorted by name, not the order they were added
expected = ">bar\nUTGCA\n>baz\nAUCTG\n>foo\nACGTU\n"
data = [('foo', ['A', 'C', 'G', 'T', 'U']),
('bar', ['U', 'T', 'G', 'C', 'A']),
('baz', ['A', 'U', 'C', 'T', 'G'])]
for contig in data:
self.genome.append_contig(contig[1], contig[0])
# Raises exception if contigs include None
# TypeError: unorderable types: NoneType() < str()
#self.genome.add_contig(None)
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle)
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_with_prefix(self):
# contigs are sorted by name, not the order they were added
expected = '>prefixbar\nUTGCA\n>prefixbaz\nAUCTG\n>prefixfoo\nACGTU\n'
data = [('foo', ['A', 'C', 'G', 'T', 'U']),
('bar', ['U', 'T', 'G', 'C', 'A']),
('baz', ['A', 'U', 'C', 'T', 'G'])]
for contig in data:
self.genome.append_contig(contig[1], contig[0])
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle, contig_prefix='prefix')
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_when_empty(self):
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle)
self.assertEqual("", handle.getvalue())
def test_send_to_fasta_handle_with_max_chars_per_line(self):
expected = '>foobarbaz\nACG\nTUA\nCGT\nUAC\nGTU\n'
self.genome.append_contig(['A', 'C', 'G', 'T', 'U'] * 3, 'foobarbaz')
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle, max_chars_per_line=3)
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_without_max_chars_per_line(self):
expected = '>foobarbaz\nACGTUACGTUACGTU\n'
self.genome.append_contig(['A', 'C', 'G', 'T', 'U'] * 3, 'foobarbaz')
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle, max_chars_per_line=0)
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_appends_to_existing_files(self):
expected = '>foo\nACGTU\n'
self.genome.append_contig(['A', 'C', 'G', 'T', 'U'], 'foo')
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle)
self.assertEqual(expected, handle.getvalue())
self.genome.send_to_fasta_handle(handle)
self.assertEqual(expected + expected, handle.getvalue())
def test_write_to_fasta_file(self):
pass
def setUp(self):
self.genome = GenomeStatus()
class GenomeStatusTestCase(unittest.TestCase):
def setUp(self):
self.genome = GenomeStatus()
def test_add_contig(self):
expected = ['foo']
self.genome.add_contig(expected[0])
self.assertEqual(expected, self.genome.get_contigs())
def test_add_contig_with_contig_name_none_raises_invalidcontigname(self):
with self.assertRaises(InvalidContigName):
self.genome.add_contig(None)
def test_add_contig_with_contig_name_empty_raises_invalidcontigname(self):
with self.assertRaises(InvalidContigName):
self.genome.add_contig("")
def test_add_contig_with_duplicate_contig_name_raises_invalidcontigname(self):
with self.assertRaises(InvalidContigName):
self.genome.add_contig('duplicate')
self.genome.add_contig('duplicate')
def test_set_current_contig_with_contig_name_none(self):
self.assertIsNone(self.genome.set_current_contig(None))
# Special case: getter behavior when argument is None
def test_set_current_contig_with_contig_name_none_returns_current_config(self):
expected = 'foo'
self.genome.add_contig(expected)
self.assertEqual(expected, self.genome.set_current_contig(None))
def test_set_current_contig_with_contig_name_invalid_and_create_contig_false_raises_invalidcontigname(self):
with self.assertRaises(InvalidContigName):
self.genome.set_current_contig('invalid_contig_name', False)
def test_set_current_contig_with_contig_name_valid_and_create_contig_false(self):
expected = 'foo'
self.genome.add_contig(expected)
self.genome.add_contig('bar')
self.assertEqual(expected, self.genome.set_current_contig(expected, False))
def test_get_contigs_empty(self):
self.assertListEqual([], self.genome.get_contigs())
def test_get_contigs(self):
expected = ['a', 'b', 'c']
# Reverse the list to verify the returned list is sorted
for contig in reversed(expected):
self.genome.add_contig(contig)
self.assertListEqual(expected, self.genome.get_contigs())
def test_append_contig_with_single_nucleotide(self):
expected = ['A']
contig_name = 'foo'
self.genome.append_contig(expected[0], contig_name)
self.assertListEqual(expected, self.genome.get_value(1, -1, contig_name))
def test_append_contig_with_list(self):
expected = ['A', 'C', 'G', 'T', 'U']
contig_name = 'foo'
self.genome.append_contig(expected, contig_name)
self.assertListEqual(expected, self.genome.get_value(1, -1, contig_name))
# TODO: make placeholder an optional final parameter
def test_extend_contig(self):
data = ['A', 'C', 'G', 'T', 'U']
placeholder = '@'
contig_name = 'foo'
expected_length = len(data) + 5
expected_content = list(data)
expected_content.extend([placeholder] * 5)
self.genome.append_contig(data, contig_name)
self.genome.extend_contig(expected_length, placeholder, contig_name)
# It allocated the additional space
self.assertEqual(expected_length, self.genome.get_contig_length(contig_name))
# It filled the allocated space after the data with the placeholder
self.assertListEqual(expected_content, self.genome.get_value(1, -1, contig_name))
def test_extend_contig_when_empty(self):
expected = 42
placeholder = '@'
contig_name = 'foo'
self.genome.add_contig(contig_name)
self.genome.extend_contig(expected, placeholder, contig_name)
# It allocated the additional space
self.assertEqual(expected, self.genome.get_contig_length(contig_name))
# It filled the undefined areas with the placeholder
self.assertListEqual([placeholder] * expected, self.genome.get_value(1, -1, contig_name))
def test_extend_contig_does_not_shrink_contig(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
expected = len(data)
placeholder = '@'
self.genome.append_contig(data, contig_name)
self.genome.extend_contig(0, placeholder, contig_name)
# It did not shrink the contig
self.assertEqual(expected, self.genome.get_contig_length(contig_name))
# It did not overwrite the existing data with a placeholder
self.assertListEqual(data, self.genome.get_value(1, -1, contig_name))
def test_set_value(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.set_value(data, 1, contig_name=contig_name)
# Given a list, it should set the range of elements beginning with the start position
self.assertListEqual(data, self.genome.get_value(1, -1, contig_name))
self.genome.set_value('A', 3, contig_name=contig_name)
data[2] = 'A'
# Given a character, it should set the element at the start position
self.assertListEqual(data, self.genome.get_value(1, -1, contig_name))
# TODO: Should it instead raise an exception?
def test_set_value_out_of_bounds(self):
contig_name = 'foo'
placeholder = '!'
expected = [placeholder] * 4
expected.append('A')
# It should fill the interim elements with the placeholder when setting an out of bounds element
self.genome.set_value('A', 5, missing_range_filler="!", contig_name=contig_name)
self.assertEqual(expected, self.genome.get_value(1, -1, contig_name))
# FIXME: get_value returns 3 data types - list, string, None
def test_get_value_with_first_position(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertEqual('A', self.genome.get_value(1, contig_name=contig_name))
def test_get_value_with_last_position(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertEqual(data, self.genome.get_value(1, -1, contig_name))
def test_get_value_empty(self):
contig_name = 'foo'
self.genome.add_contig(contig_name)
self.assertEqual([], self.genome.get_value(1, contig_name=contig_name))
def test_get_value_with_contig_name_invalid(self):
self.assertEqual([], self.genome.get_value(1, contig_name='invalid'))
def test_get_value_with_invalid_position_raises_indexerror(self):
with self.assertRaises(IndexError):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.genome.get_value(0, contig_name=contig_name)
def test_get_value_range_of_one(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertListEqual(['C'], self.genome.get_value(2, 2, contig_name))
def test_get_value_reversed_position_values(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(data, contig_name)
self.assertEqual([], self.genome.get_value(2, 1, contig_name=contig_name))
# TODO: Could this hide index errors?
def test_get_value_outside_range(self):
contig_name = 'foo'
expected = ['A', 'C', 'G', 'T', 'U']
self.genome.append_contig(expected, contig_name)
self.assertListEqual(expected, self.genome.get_value(1, 10, contig_name=contig_name))
# TODO: Is there a conflict if there are different placeholders?
# Example: contig_extend fills allocated region with placeholder A,
# but get_value retrieves an even larger region filling it with placeholder B
# the result might be: [d,a,t,a,A,A,A,A,B,B,B,B]
def test_get_value_outside_range_with_filler(self):
contig_name = 'foo'
placeholder = '@'
data = ['A', 'C', 'G', 'T', 'U']
expected = list(data)
expected.extend([placeholder] * 5)
self.genome.append_contig(data, contig_name)
# It should fill out of bounds region with the placeholder
self.assertListEqual(expected, self.genome.get_value(1, 10, contig_name=contig_name, placeholder=placeholder))
def test_get_contig_length(self):
contig_name = 'foo'
data = ['A', 'C', 'G', 'T', 'U']
self.genome.add_contig(contig_name)
self.genome.append_contig(data, contig_name)
self.assertEqual(len(data), self.genome.get_contig_length(contig_name))
def test_get_contig_length_when_empty(self):
contig_name = 'foo'
self.genome.add_contig(contig_name)
self.assertEqual(0, self.genome.get_contig_length(contig_name))
def test_get_contig_length_with_contig_name_invalid(self):
self.assertEqual(0, self.genome.get_contig_length('invalid'))
def test_get_contig_length_with_contig_name_none(self):
# FIXME: test fails without self.genome.add_contig(None)
self.assertEqual(0, self.genome.get_contig_length(None))
def test_send_to_fasta_handle(self):
# contigs are sorted by name, not the order they were added
expected = ">bar\nUTGCA\n>baz\nAUCTG\n>foo\nACGTU\n"
data = [
('foo', ['A', 'C', 'G', 'T', 'U']),
('bar', ['U', 'T', 'G', 'C', 'A']),
('baz', ['A', 'U', 'C', 'T', 'G'])
]
for contig in data:
self.genome.append_contig(contig[1], contig[0])
# Raises exception if contigs include None
# TypeError: unorderable types: NoneType() < str()
#self.genome.add_contig(None)
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle)
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_with_prefix(self):
# contigs are sorted by name, not the order they were added
expected = '>prefixbar\nUTGCA\n>prefixbaz\nAUCTG\n>prefixfoo\nACGTU\n'
data = [
('foo', ['A', 'C', 'G', 'T', 'U']),
('bar', ['U', 'T', 'G', 'C', 'A']),
('baz', ['A', 'U', 'C', 'T', 'G'])
]
for contig in data:
self.genome.append_contig(contig[1], contig[0])
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle, contig_prefix='prefix')
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_when_empty(self):
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle)
self.assertEqual("", handle.getvalue())
def test_send_to_fasta_handle_with_max_chars_per_line(self):
expected = '>foobarbaz\nACG\nTUA\nCGT\nUAC\nGTU\n'
self.genome.append_contig(['A', 'C', 'G', 'T', 'U'] * 3, 'foobarbaz')
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle, max_chars_per_line=3)
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_without_max_chars_per_line(self):
expected = '>foobarbaz\nACGTUACGTUACGTU\n'
self.genome.append_contig(['A', 'C', 'G', 'T', 'U'] * 3, 'foobarbaz')
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle, max_chars_per_line=0)
self.assertEqual(expected, handle.getvalue())
def test_send_to_fasta_handle_appends_to_existing_files(self):
expected = '>foo\nACGTU\n'
self.genome.append_contig(['A', 'C', 'G', 'T', 'U'], 'foo')
with StringIO() as handle:
self.genome.send_to_fasta_handle(handle)
self.assertEqual(expected, handle.getvalue())
self.genome.send_to_fasta_handle(handle)
self.assertEqual(expected + expected, handle.getvalue())
def test_write_to_fasta_file(self):
pass
def setUp(self):
self.genome = GenomeStatus()
