1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260 | #(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)
"""
This module provides PermutationContainer class
which parses files, stores permutations and
provides some other usefull functions
"""
from __future__ import absolute_import
from __future__ import division
from collections import defaultdict
import logging
import os
from copy import deepcopy
from ragout.shared.debug import DebugConfig
from ragout.shared import config
from ragout.shared.datatypes import Block, Permutation, output_permutations
import ragout.breakpoint_graph.repeat_resolver as rr
from ragout.six.moves import filter
logger = logging.getLogger()
debugger = DebugConfig.get_instance()
class PermException(Exception):
pass
class PermutationContainer:
def __init__(self, block_coords_file, recipe,
resolve_repeats, allow_ref_indels, phylogeny):
"""
Parses permutation files referenced from recipe and filters duplications
"""
self.ref_perms = []
self.target_perms = []
self.recipe = recipe
logging.info("Reading %s", block_coords_file)
permutations = _parse_blocks_coords(block_coords_file)
has_sequences = set()
draft_names = set()
for p in permutations:
if p.genome_name not in recipe["genomes"]:
continue
p.draft = recipe["genomes"][p.genome_name]["draft"]
if p.draft:
draft_names.add(p.genome_name)
has_sequences.add(p.genome_name)
if p.genome_name == recipe["target"]:
self.target_perms.append(p)
else:
self.ref_perms.append(p)
for genome in recipe["genomes"]:
if genome not in has_sequences:
raise PermException("No sequences read for genome {0}. Check "
"recipe for correctness.".format(genome))
_check_coverage(self.ref_perms + self.target_perms)
logger.debug("Read %d reference sequences", len(self.ref_perms))
if not len(self.ref_perms):
raise PermException("No synteny blocks found in "
"reference sequences")
logger.debug("Read %d target sequences", len(self.target_perms))
if not len(self.target_perms):
raise PermException("No synteny blocks found in "
"target sequences")
self._filter_indels(allow_ref_indels)
logger.debug("%d target sequences left after indel filtering",
len(self.target_perms))
repeats = _find_repeats(self.ref_perms + self.target_perms)
###
if resolve_repeats:
if phylogeny is None:
raise PermException("Resolving repeats with "
"yet unknown phylogeny")
rr.resolve_repeats(self.ref_perms, self.target_perms,
repeats, phylogeny, draft_names)
###
self._filter_repeats(repeats)
logger.debug("%d target sequences left after repeat filtering",
len(self.target_perms))
if not len(self.target_perms):
raise PermException("No synteny blocks found in the target "
"genome after repeat/indel filtering.")
if debugger.debugging:
filtered_file = os.path.join(debugger.debug_dir, "filtered_contigs.txt")
output_permutations(self.target_perms, filtered_file)
def _filter_indels(self, allow_ref_indels):
"""
Keep only blocks that appear in target and
all references (or one reference, if allow_ref_indels is set)
"""
multiplicity = defaultdict(int)
target_blocks = set()
reference_blocks = set()
def process(perms, block_set):
for perm in perms:
for block in perm.blocks:
multiplicity[block.block_id] += 1
block_set.add(block.block_id)
process(self.target_perms, target_blocks)
process(self.ref_perms, reference_blocks)
if allow_ref_indels:
to_keep = target_blocks.intersection(reference_blocks)
else:
num_genomes = len(self.recipe["genomes"])
#to_keep = set(filter(lambda b: multiplicity[b] >= num_genomes,
# multiplicity))
to_keep = set([b for b in multiplicity if multiplicity[b] >= num_genomes])
self.ref_perms = _filter_permutations(self.ref_perms, to_keep)
self.target_perms = _filter_permutations(self.target_perms, to_keep)
def _filter_repeats(self, repeats):
"""
Filters repetitive blocks
"""
self.target_perms = _filter_permutations(self.target_perms, repeats,
inverse=True)
self.ref_perms = _filter_permutations(self.ref_perms, repeats,
inverse=True)
def _find_repeats(permutations):
"""
Returns a set of repetitive blocks
"""
index = defaultdict(set)
repeats = set()
for perm in permutations:
for block in perm.blocks:
if perm.genome_name in index[block.block_id]:
repeats.add(block.block_id)
else:
index[block.block_id].add(perm.genome_name)
return repeats
def _filter_permutations(permutations, blocks, inverse=False):
"""
Filters given blocks from permutations
"""
new_perms = []
filter_func = lambda b: (b.block_id in blocks) != inverse
for perm in permutations:
new_blocks = list(filter(filter_func, perm.blocks))
if new_blocks:
new_perms.append(deepcopy(perm))
new_perms[-1].blocks = new_blocks
return new_perms
def _parse_blocks_coords(filename):
"""
Parses a file with blocks coords
"""
perm_by_id = {}
with open(filename, "r") as f:
header = True
for line in f:
line = line.strip()
if not line:
continue
if header:
if line.startswith("Seq_id"):
continue
if line.startswith("-"):
header = False
continue
chr_id, chr_size, seq_name = line.split("\t")
tokens = seq_name.split(".", 1)
if len(tokens) != 2:
raise PermException("permutation ids in " + filename +
" do not follow naming convention: " +
"'genome.chromosome'")
genome_name, chr_name = tokens
perm_by_id[chr_id] = Permutation(genome_name, chr_name,
int(chr_size), [])
else:
if line.startswith("Seq_id") or line.startswith("-"):
continue
if line.startswith("Block"):
block_id = int(line.split(" ")[1][1:])
continue
seq_id, sign, start, end, _length = line.split("\t")
if sign == "-":
start, end = end, start
if int(end) < int(start):
raise PermException("Error in permutations file format")
sign_num = 1 if sign == "+" else -1
perm_by_id[seq_id].blocks.append(Block(block_id, sign_num,
int(start), int(end)))
for perm in perm_by_id.values():
perm.blocks.sort(key=lambda b: b.start)
#out_perms = list(filter(lambda b: len(b.blocks), perm_by_id.values()))
out_perms = [b for b in perm_by_id.values() if len(b.blocks)]
if not len(out_perms):
raise PermException("Permutations file is empty")
return out_perms
def _check_coverage(permutations):
"""
Checks if synteny blocks coverage is acceptable
"""
by_genome = defaultdict(list)
for perm in permutations:
by_genome[perm.genome_name].append(perm)
warning_genomes = []
for genome_name, genome_perms in by_genome.items():
total_length = 0
total_covered = 0
for perm in genome_perms:
total_length += perm.length()
for block in perm.blocks:
total_covered += block.length()
coverage = float(total_covered) / total_length
logger.info("\"{0}\" synteny blocks coverage: {1:2.4}%"
.format(genome_name, 100 * coverage))
if coverage < config.vals["min_synteny_coverage"]:
warning_genomes.append((genome_name, coverage))
if warning_genomes:
#for genome_name, coverage in warning_genomes:
# logger.warning("\"{0}\" synteny blocks coverage: {1:2.4}%"
# .format(genome_name, 100 * coverage))
logger.warning("Some genomes have low synteny block coverage "
"- results can be inaccurate. "
"Possible reasons: \n"
"\t1. Genome is too distant from others\n"
"\t2. Synteny block parameters are chosen incorrectly"
"\n\tTry to change synteny blocks paramsters or "
"remove this genome from the comparison")
|