def test_contig_coords(self):
'''contig_coords() should get the coords of all contigs in a sequence correctly'''
test_seqs = [
fastn.Fasta('ID', 'ACGT'),
fastn.Fasta('ID', 'NACGT'),
fastn.Fasta('ID', 'NNACGT'),
fastn.Fasta('ID', 'ACGTN'),
fastn.Fasta('ID', 'ACGTNN'),
fastn.Fasta('ID', 'NANNCGT'),
fastn.Fasta('ID', 'ANNCGTNNAAAAA')
]
correct_coords = [[genome_intervals.Interval(0, 3)],
[genome_intervals.Interval(1, 4)],
[genome_intervals.Interval(2, 5)],
[genome_intervals.Interval(0, 3)],
[genome_intervals.Interval(0, 3)],
[
genome_intervals.Interval(1, 1),
genome_intervals.Interval(4, 6)
],
[
genome_intervals.Interval(0, 0),
genome_intervals.Interval(3, 5),
genome_intervals.Interval(8, 12)
]]
for i in range(len(test_seqs)):
gaps = test_seqs[i].contig_coords()
self.assertListEqual(correct_coords[i], gaps)
def test_intersection(self):
'''Intersection should either return None or the correct intersection'''
a = genome_intervals.Interval(5, 10)
b = genome_intervals.Interval(8, 15)
c = genome_intervals.Interval(12, 20)
self.assertEqual(a.intersection(c), None)
self.assertEqual(a.intersection(b), genome_intervals.Interval(8, 10))
def test_length_sum_from_list(self):
'''Test that total length of intervals is summed correctly'''
a = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(4, 5),
genome_intervals.Interval(10, 19)
]
self.assertEqual(14, genome_intervals.length_sum_from_list(a))
def test_init(self):
'''Throw error if try to construct genome_interval from a non-int, or end<start'''
with self.assertRaises(genome_intervals.Error):
genome_intervals.Interval('a', 1)
with self.assertRaises(genome_intervals.Error):
genome_intervals.Interval(1, 'a')
with self.assertRaises(genome_intervals.Error):
genome_intervals.Interval('a', 'a')
with self.assertRaises(genome_intervals.Error):
genome_intervals.Interval(3, 2)
def test_comparisons(self):
'''< and <= should work as expected'''
self.assertTrue(
genome_intervals.Interval(1, 2) < genome_intervals.Interval(2, 2))
self.assertTrue(
genome_intervals.Interval(1, 2) <= genome_intervals.Interval(2, 2))
self.assertFalse(
genome_intervals.Interval(2, 2) <= genome_intervals.Interval(1, 2))
self.assertFalse(
genome_intervals.Interval(2, 2) < genome_intervals.Interval(1, 2))
self.assertFalse(
genome_intervals.Interval(2, 2) < genome_intervals.Interval(2, 2))
def test_union_flll_gap(self):
'''union_fill_gap() should ignore intersections and return the maximum range of coords'''
a = genome_intervals.Interval(5, 10)
b = genome_intervals.Interval(8, 15)
c = genome_intervals.Interval(12, 20)
d = genome_intervals.Interval(21, 22)
self.assertEqual(a.union_fill_gap(c), genome_intervals.Interval(5, 20))
self.assertEqual(c.union_fill_gap(a), genome_intervals.Interval(5, 20))
self.assertEqual(a.union_fill_gap(b), genome_intervals.Interval(5, 15))
self.assertEqual(b.union_fill_gap(a), genome_intervals.Interval(5, 15))
self.assertEqual(c.union_fill_gap(d),
genome_intervals.Interval(12, 22))
self.assertEqual(d.union_fill_gap(c),
genome_intervals.Interval(12, 22))
def gaps(self, min_length=1):
gaps = []
regex = re.compile('N+', re.IGNORECASE)
for m in regex.finditer(self.seq):
if m.span()[1] - m.span()[0] + 1 >= min_length:
gaps.append(
genome_intervals.Interval(m.span()[0],
m.span()[1] - 1))
return gaps
def test_union(self):
'''Union should either return None or the correct union'''
a = genome_intervals.Interval(5, 10)
b = genome_intervals.Interval(8, 15)
c = genome_intervals.Interval(12, 20)
d = genome_intervals.Interval(21, 22)
self.assertEqual(a.union(c), None)
self.assertEqual(c.union(a), None)
self.assertEqual(a.union(b), genome_intervals.Interval(5, 15))
self.assertEqual(b.union(a), genome_intervals.Interval(5, 15))
self.assertEqual(c.union(d), genome_intervals.Interval(12, 22))
self.assertEqual(d.union(c), genome_intervals.Interval(12, 22))
def test_merge_overlapping_in_list(self):
'''merge_overlapping_in_list() merges correctly'''
a = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(51, 60),
genome_intervals.Interval(10, 20),
genome_intervals.Interval(20, 30),
genome_intervals.Interval(20, 30),
genome_intervals.Interval(29, 50),
genome_intervals.Interval(65, 70)
]
b = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(10, 60),
genome_intervals.Interval(65, 70)
]
genome_intervals.merge_overlapping_in_list(a)
self.assertSequenceEqual(a, b)
def contig_coords(self):
# contigs are the opposite of gaps, so work out the coords from the gap coords
gaps = self.gaps()
if len(gaps) == 0:
return [genome_intervals.Interval(0, len(self) - 1)]
coords = [0]
for g in gaps:
if g.start == 0:
coords = [g.end + 1]
else:
coords += [g.start - 1, g.end + 1]
if coords[-1] + 1 < len(self):
coords.append(len(self) - 1)
return [
genome_intervals.Interval(coords[i], coords[i + 1])
for i in range(0,
len(coords) - 1, 2)
]
def get_nucmer_hits(coords_file):
qry_hits = {}
ref_hits = {}
nucmer_reader = nucmer.file_reader(coords_file)
for hit in nucmer_reader:
# nucmer hits are 1-based. INside the script, use 0-based.
start, end = sorted([hit.ref_start - 1, hit.ref_end - 1])
if hit.ref_name not in ref_hits:
ref_hits[hit.ref_name] = []
ref_hits[hit.ref_name].append(genome_intervals.Interval(start, end))
start, end = sorted([hit.qry_start - 1, hit.qry_end - 1])
if hit.qry_name not in qry_hits:
qry_hits[hit.qry_name] = []
qry_hits[hit.qry_name].append(genome_intervals.Interval(start, end))
for l in ref_hits.values():
genome_intervals.merge_overlapping_in_list(l)
for l in qry_hits.values():
genome_intervals.merge_overlapping_in_list(l)
return ref_hits, qry_hits
def file2regions(fname):
regions = {}
f = utils.open_file_read(fname)
for line in f:
if line.startswith('#'):
continue
(chr, start, end) = line.rstrip().split()
if chr not in regions:
regions[chr] = []
regions[chr].append(genome_intervals.Interval(start, end))
utils.close(f)
return regions
def test_intersects(self):
'''Intersection of two intervals should do the right thing'''
a = genome_intervals.Interval(5, 10)
no_intersect = [
genome_intervals.Interval(3, 4),
genome_intervals.Interval(11, 20)
]
intersect = [
genome_intervals.Interval(3, 5),
genome_intervals.Interval(3, 6),
genome_intervals.Interval(9, 12),
genome_intervals.Interval(10, 12),
genome_intervals.Interval(6, 7),
genome_intervals.Interval(1, 20)
]
for i in no_intersect:
self.assertFalse(a.intersects(i),
'shouldn\'t intersect: ' + str(a) + ', ' + str(i))
for i in intersect:
self.assertTrue(a.intersects(i),
'should intersect: ' + str(a) + ', ' + str(i))
def test_gaps(self):
'''gaps() should find the gaps in a sequence correctly'''
test_seqs = [
fastn.Fasta('ID', 'ACGT'),
fastn.Fasta('ID', 'NACGT'),
fastn.Fasta('ID', 'NACGTN'),
fastn.Fasta('ID', 'ANNCGT'),
fastn.Fasta('ID', 'NANNCGTNN')
]
correct_gaps = [[], [genome_intervals.Interval(0, 0)],
[
genome_intervals.Interval(0, 0),
genome_intervals.Interval(5, 5)
], [genome_intervals.Interval(1, 2)],
[
genome_intervals.Interval(0, 0),
genome_intervals.Interval(2, 3),
genome_intervals.Interval(7, 8)
]]
for i in range(len(test_seqs)):
gaps = test_seqs[i].gaps()
self.assertListEqual(correct_gaps[i], gaps)
if not sam_record.is_forward_strand():
sam_record.cigar.reverse()
hit_start = 1
hit_end = len(sam_record.seq)
if sam_record.cigar.operations[0].operator == 'S':
hit_start = sam_record.cigar.operations[0].number
if sam_record.cigar.operations[-1].operator == 'S':
hit_end = len(sam_record.seq) - sam_record.cigar.operations[-1].number
if sam_record.id not in read_hit_coords:
read_hit_coords[sam_record.id] = []
read_hit_coords[sam_record.id].append(genome_intervals.Interval(hit_start - 1, hit_end - 1))
external_progs.bwa_index_clean(bwa_index)
os.unlink(bwa_sam)
seq_reader = fastn.file_reader(options.reads_in)
f_fa = utils.open_file_write(options.outprefix + '.fq')
f_log = utils.open_file_write(options.outprefix + '.log')
for seq in seq_reader:
if seq.id not in read_hit_coords:
print(seq, file=f_fa)
print(seq.id, 'no hit', sep='\t', file=f_log)
else:
hits = read_hit_coords[seq.id]
d['step'] = int(step)
return d
delete_range = range2dic(options.delete_range)
insert_range = range2dic(options.insert_range)
# convert the -d regions into sequence name, start and end coords
to_delete = {}
if options.delete:
for s in options.delete:
id, coords = s.rsplit(':')
start, end = [int(x) - 1 for x in coords.split('-')]
if id not in to_delete:
to_delete[id] = []
to_delete[id].append(genome_intervals.Interval(start, end))
to_insert = {}
if options.insert:
for s in options.insert:
id, pos, bases = s.rsplit(':', 2)
pos = int(pos) - 1
bases = int(bases)
if id not in to_insert:
to_insert[id] = []
to_insert[id].append((pos, bases))
assert len(to_delete) * len(to_insert) == 0
# merge overlapping regions to be deleted
for l in to_delete.values():
def test_contains(self):
'''Check that contains() works as expected'''
a = genome_intervals.Interval(5, 10)
not_contained = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(4, 5),
genome_intervals.Interval(4, 10),
genome_intervals.Interval(4, 11),
genome_intervals.Interval(5, 11),
genome_intervals.Interval(1, 2),
genome_intervals.Interval(9, 11),
genome_intervals.Interval(10, 11),
genome_intervals.Interval(11, 20)
]
contained = [
genome_intervals.Interval(5, 5),
genome_intervals.Interval(5, 10),
genome_intervals.Interval(6, 7),
genome_intervals.Interval(6, 10),
genome_intervals.Interval(10, 10)
]
for i in not_contained:
self.assertFalse(a.contains(i),
'shouldn\'t contain: ' + str(a) + ', ' + str(i))
for i in contained:
self.assertTrue(a.contains(i),
'should contain: ' + str(a) + ', ' + str(i))
def test_len(self):
self.assertEqual(len(genome_intervals.Interval(1, 2)), 2)
self.assertEqual(len(genome_intervals.Interval(1, 1)), 1)
self.assertEqual(len(genome_intervals.Interval(10, 20)), 11)
# load hits into hash. key=ref_name, value=another hash with key=qry_name, value=list of hit positions in that ref seq
nucmer_hits = {}
contigs_to_print = {}
nucmer_reader = nucmer.file_reader(nucmer_out_coords)
for hit in nucmer_reader:
if hit.ref_name not in nucmer_hits:
nucmer_hits[hit.ref_name] = {}
if hit.qry_name not in nucmer_hits[hit.ref_name]:
nucmer_hits[hit.ref_name][hit.qry_name] = []
nucmer_hits[hit.ref_name][hit.qry_name].append(
genome_intervals.Interval(min(hit.ref_start, hit.ref_end),
max(hit.ref_start, hit.ref_end)))
# merge all the overalpping hits for each list of hits corresponding to one contig
for ref_name, d in nucmer_hits.items():
for qry_name, hits in d.items():
genome_intervals.merge_overlapping_in_list(hits)
for hit in hits:
if hit.end - hit.start + 1 >= options.min_seq_length:
if ref_name not in contigs_to_print:
contigs_to_print[ref_name] = []
contigs_to_print[ref_name].append(copy.copy(hit))
# remove any contigs that are completely contained in another contig
for ref, l in contigs_to_print.items():
# get query sequence lengths and gap positions - add each gap coord to the
# list of covered positions for each sequence
for seq in seq_reader:
assert seq.id not in seq_lengths
seq_lengths[seq.id] = len(seq)
covered_regions[seq.id] = seq.gaps()
nucmer_reader = nucmer.file_reader(options.nucmer_coords)
for hit in nucmer_reader:
assert hit.qry_name in seq_lengths
# gaps are stored with coords starting from zero. Nucmer starts at 1, so need to decrement the coords
start, end = sorted([hit.qry_start - 1, hit.qry_end - 1])
covered_regions[hit.qry_name].append(genome_intervals.Interval(start, end))
# merge the covered regions
for l in covered_regions.values():
genome_intervals.merge_overlapping_in_list(l)
f = utils.open_file_write(options.outfile)
# get the regions that are not covered
for id, covered in covered_regions.items():
not_covered = []
if len(covered) == 0:
not_covered = [[1, seq_lengths[id]]]
else:
if covered[0].start != 0:
def test_remove_contained_in_list(self):
'''test_remove_contained_in_list removes the right elements of list'''
a = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(4, 4),
genome_intervals.Interval(4, 5),
genome_intervals.Interval(5, 6),
genome_intervals.Interval(7, 9),
genome_intervals.Interval(8, 10),
genome_intervals.Interval(9, 11),
genome_intervals.Interval(20, 25),
genome_intervals.Interval(20, 24),
genome_intervals.Interval(20, 26),
genome_intervals.Interval(30, 38),
genome_intervals.Interval(30, 37),
genome_intervals.Interval(30, 36),
genome_intervals.Interval(30, 35),
genome_intervals.Interval(30, 35),
genome_intervals.Interval(32, 33),
genome_intervals.Interval(38, 50),
genome_intervals.Interval(65, 70),
genome_intervals.Interval(67, 70)
]
b = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(4, 5),
genome_intervals.Interval(5, 6),
genome_intervals.Interval(7, 9),
genome_intervals.Interval(8, 10),
genome_intervals.Interval(9, 11),
genome_intervals.Interval(20, 26),
genome_intervals.Interval(30, 38),
genome_intervals.Interval(38, 50),
genome_intervals.Interval(65, 70)
]
genome_intervals.remove_contained_in_list(a)
self.assertSequenceEqual(a, b)
def test_intersection(self):
'''intersection() should correctly intersect two lists of intervals'''
a = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(10, 20),
genome_intervals.Interval(51, 52),
genome_intervals.Interval(54, 55),
genome_intervals.Interval(57, 58)
]
b = [
genome_intervals.Interval(5, 6),
genome_intervals.Interval(9, 11),
genome_intervals.Interval(13, 14),
genome_intervals.Interval(17, 18),
genome_intervals.Interval(20, 25),
genome_intervals.Interval(50, 60)
]
i = [
genome_intervals.Interval(10, 11),
genome_intervals.Interval(13, 14),
genome_intervals.Interval(17, 18),
genome_intervals.Interval(20, 20),
genome_intervals.Interval(51, 52),
genome_intervals.Interval(54, 55),
genome_intervals.Interval(57, 58)
]
self.assertSequenceEqual(genome_intervals.intersection(a, b), i)
self.assertSequenceEqual(genome_intervals.intersection(b, a), i)
'Makes a random genome with sequence lengths and names determined by an fai file. IMPORTANT: not really random, at the moment every base will be an A (or an N if --gaps_file used)',
usage='%(prog)s [options] <fai file> <outfile>')
parser.add_argument(
'--gaps_file',
help='File of gaps, each line in the form: "chr start end" (tab separated)'
)
parser.add_argument('fai_file', help='Name of fai file')
parser.add_argument('outfile', help='Name of output fasta file')
options = parser.parse_args()
gaps = {}
if options.gaps_file:
f = utils.open_file_read(options.gaps_file)
for line in f:
(id, start, end) = line.rstrip().split('\t')
gap = genome_intervals.Interval(int(start) - 1, int(end) - 1)
if id not in gaps:
gaps[id] = []
gaps[id].append(gap)
utils.close(f)
f_in = utils.open_file_read(options.fai_file)
f_out = utils.open_file_write(options.outfile)
for line in f_in:
a = line.rstrip().split()
fa = fastn.Fasta(a[0], 'A' * int(a[1]))
if fa.id in gaps:
fa.seq = list(fa.seq)
for gap in gaps[fa.id]:
