def test_merge_overlapping_in_list(self):
"""merge_overlapping_in_list() merges correctly"""
a = [
intervals.Interval(1, 2),
intervals.Interval(51, 60),
intervals.Interval(10, 20),
intervals.Interval(20, 30),
intervals.Interval(20, 30),
intervals.Interval(29, 50),
intervals.Interval(65, 70),
]
b = [intervals.Interval(1, 2), intervals.Interval(10, 60), intervals.Interval(65, 70)]
intervals.merge_overlapping_in_list(a)
self.assertSequenceEqual(a, b)
def test_merge_overlapping_in_list(self):
'''merge_overlapping_in_list() merges correctly'''
a = [
intervals.Interval(1, 2),
intervals.Interval(51, 60),
intervals.Interval(10, 20),
intervals.Interval(20, 30),
intervals.Interval(20, 30),
intervals.Interval(29, 50),
intervals.Interval(65, 70)
]
b = [
intervals.Interval(1, 2),
intervals.Interval(10, 60),
intervals.Interval(65, 70)
]
intervals.merge_overlapping_in_list(a)
self.assertSequenceEqual(a, b)
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(
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():
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():
intervals.remove_contained_in_list(l)
# print the final perfect contigs
f_out = utils.open_file_write(options.outprefix + '.fa')
counter = 1
def run(description):
parser = argparse.ArgumentParser(
description=description,
usage='fastaq add_indels [options] <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
parser.add_argument(
'-d',
'--delete',
action='append',
help=
'Delete the given bases from the given sequence. Format same as samtools view: name:start-end. This option can be used multiple times (once for each region to delete). Overlapping coords will be merged before deleting',
metavar='Name:start:bases')
parser.add_argument(
'--delete_range',
help=
'Deletes bases starting at position P in each sequence of the input file. Deletes start + (n-1)*step bases from sequence n.',
metavar='P,start,step')
parser.add_argument(
'-i',
'--insert',
action='append',
help=
'Insert a random string of bases at the given position. Format is name:position:number_to_add. Bases are added after the position. This option can be used multiple times',
metavar='Name:start:bases')
parser.add_argument(
'--insert_range',
help=
'Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.',
metavar='P,start,step')
options = parser.parse_args()
test_ops = [
int(x is not None) for x in [
options.delete, options.insert, options.delete_range,
options.insert_range
]
]
if sum(test_ops) != 1:
print(
'Must use one of --delete, --insert, --delete_range, --insert_range. Cannot continue',
file=sys.stderr)
sys.exit(1)
def range2dic(range_in):
if range_in is None:
return {}
(pos, start, step) = range_in.split(',')
d = {}
d['pos'] = int(pos) - 1
d['bases'] = int(start)
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(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():
intervals.merge_overlapping_in_list(l)
# sort positions to be inserted
for l in to_insert.values():
l.sort()
# read in the fasta/q file and print outfile with deleted sequences
seq_reader = sequences.file_reader(options.infile)
f = utils.open_file_write(options.outfile)
for seq in seq_reader:
if seq.id in to_delete:
# delete regions for this sequence, but start at the end so the
# coords don't get messed up after the first deletion
for inter in reversed(to_delete[seq.id]):
seq.seq = seq.seq[:inter.start] + seq.seq[inter.end + 1:]
elif options.delete_range:
seq.seq = seq.seq[:delete_range['pos']] + seq.seq[
delete_range['pos'] + delete_range['bases']:]
delete_range['bases'] += delete_range['step']
elif seq.id in to_insert:
for pos, bases in reversed(to_insert[seq.id]):
seq.seq = seq.seq[:pos + 1] + ''.join(
[random.choice('ACGT')
for x in range(bases)]) + seq.seq[pos + 1:]
elif options.insert_range:
seq.seq = seq.seq[:insert_range['pos'] + 1] + ''.join([
random.choice('ACGT') for x in range(insert_range['bases'])
]) + seq.seq[insert_range['pos'] + 1:]
insert_range['bases'] += insert_range['step']
print(seq, file=f)
utils.close(f)
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(
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():
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():
intervals.remove_contained_in_list(l)
# print the final perfect contigs
f_out = utils.open_file_write(options.outprefix + ".fa")
counter = 1
def run(description):
parser = argparse.ArgumentParser(
description = description,
usage = 'fastaq add_indels [options] <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
parser.add_argument('-d','--delete', action='append', help='Delete the given bases from the given sequence. Format same as samtools view: name:start-end. This option can be used multiple times (once for each region to delete). Overlapping coords will be merged before deleting', metavar='Name:start:bases')
parser.add_argument('--delete_range', help='Deletes bases starting at position P in each sequence of the input file. Deletes start + (n-1)*step bases from sequence n.', metavar='P,start,step')
parser.add_argument('-i','--insert', action='append', help='Insert a random string of bases at the given position. Format is name:position:number_to_add. Bases are added after the position. This option can be used multiple times', metavar='Name:start:bases')
parser.add_argument('--insert_range', help='Inserts random bases starting after position P in each sequence of the input file. Inserts start + (n-1)*step bases into sequence n.', metavar='P,start,step')
options = parser.parse_args()
test_ops = [int(x is not None) for x in [options.delete, options.insert, options.delete_range, options.insert_range]]
if sum(test_ops) != 1:
print('Must use one of --delete, --insert, --delete_range, --insert_range. Cannot continue', file=sys.stderr)
sys.exit(1)
def range2dic(range_in):
if range_in is None:
return {}
(pos, start, step) = range_in.split(',')
d = {}
d['pos'] = int(pos) - 1
d['bases'] = int(start)
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(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():
intervals.merge_overlapping_in_list(l)
# sort positions to be inserted
for l in to_insert.values():
l.sort()
# read in the fasta/q file and print outfile with deleted sequences
seq_reader = sequences.file_reader(options.infile)
f = utils.open_file_write(options.outfile)
for seq in seq_reader:
if seq.id in to_delete:
# delete regions for this sequence, but start at the end so the
# coords don't get messed up after the first deletion
for inter in reversed(to_delete[seq.id]):
seq.seq = seq.seq[:inter.start] + seq.seq[inter.end + 1:]
elif options.delete_range:
seq.seq = seq.seq[:delete_range['pos']] + seq.seq[delete_range['pos'] + delete_range['bases']:]
delete_range['bases'] += delete_range['step']
elif seq.id in to_insert:
for pos, bases in reversed(to_insert[seq.id]):
seq.seq = seq.seq[:pos + 1] + ''.join([random.choice('ACGT') for x in range(bases)]) + seq.seq[pos + 1:]
elif options.insert_range:
seq.seq = seq.seq[:insert_range['pos'] + 1] + ''.join([random.choice('ACGT') for x in range(insert_range['bases'])]) + seq.seq[insert_range['pos'] + 1:]
insert_range['bases'] += insert_range['step']
print(seq, file=f)
utils.close(f)