-
Notifications
You must be signed in to change notification settings - Fork 50
/
ragtag_merge.py
430 lines (347 loc) · 16.3 KB
/
ragtag_merge.py
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
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
#!/usr/bin/env python
"""
MIT License
Copyright (c) 2021 Michael Alonge <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""
import os
import sys
import argparse
import networkx as nx
import numpy as np
from ragtag_utilities.AGPFile import AGPFile
from ragtag_utilities.ScaffoldGraph import ScaffoldGraphBase
from ragtag_utilities.ScaffoldGraph import MultiScaffoldGraph
from ragtag_utilities.ScaffoldGraph import AGPMultiScaffoldGraph
from ragtag_utilities.RestrictionFragmentMap import RestrictionEnzymes
from ragtag_utilities.utilities import log, get_ragtag_version, run_oae
def build_hic_graph(hic_file, components_fasta_fname):
G = MultiScaffoldGraph(components_fasta_fname)
# Iterate over the hic links and build the salsa graph
with open(hic_file, "r") as f:
for line in f:
fields = line.rstrip().split("\t")
n1, n2, w = fields[0], fields[1], float(fields[2])
G.add_edge(
n1,
n2,
weight=w,
source_fname=hic_file,
is_known_gap_size=False,
gap_size=100,
gap_type="scaffold",
linkage=True,
linkage_evidence="proximity_ligation"
)
SG = G.merge()
return SG.best_buddy_scale()
def get_maximal_matching(sg):
""" Find a scaffolding solution given a Scaffold Graph"""
matching = sg.get_max_weight_matching()
cover_graph = nx.Graph()
cover_graph.add_nodes_from(sg.nodes(data=True))
# Add edges connecting contig ends
node_base_set = set([i[:-2] for i in list(cover_graph.nodes)])
for node in node_base_set:
cover_graph.add_edge(node + "_b", node + "_e", weight=np.inf)
# Add the Scaffold Graph edges that form the matching
for u, v in matching:
cover_graph.add_edge(u, v, **sg[u][v])
# Remove any potential cycles
edges_to_delete = []
for cc in nx.connected_components(G=cover_graph):
cc = cover_graph.subgraph(cc).copy()
if cc.number_of_nodes() == cc.number_of_edges():
assembly_edges = cc.edges(data=True)
edges_to_delete.append(min(assembly_edges, key=lambda entry: entry[2]["weight"]))
for u, v, data in edges_to_delete:
cover_graph.remove_edge(u, v)
return cover_graph
def get_gap_size(size_list, func):
if func not in {"MIN", "MAX", "MEAN"}:
raise ValueError("{} not a valid function for determining gap size".format(func))
if func == "MIN":
return min(size_list)
if func == "MAX":
return max(size_list)
return int(np.mean(size_list))
def write_agp_solution(cover_graph, scaffold_graph, agp_fname, gap_func="MIN", add_suffix_to_unplaced=False):
"""
Here, we work with two graphs: A cover_graph and a scaffold_graph. A covergrpah defines a solution to the scaffold
graph, and nodes from the same component are connected for convenience.
We use the scaffold_graph for any original scaffold_graph info/functionality
"""
if not isinstance(scaffold_graph, ScaffoldGraphBase):
raise TypeError("scaffold_graph must be an instance of ScaffoldGraph")
placed_components = set()
# Iterate over each connected component
agp = AGPFile(agp_fname, mode="w")
agp.add_pragma()
agp.add_comment("# AGP created by RagTag {}".format(get_ragtag_version()))
# Iterate through the connected components
for i, cc in enumerate(nx.connected_components(G=cover_graph)):
# Sort the list of nodes for deterministic output
cc = sorted(list(cc))
obj_header = "scf" + "{0:08}".format(i+1) + "_RagTag"
current_node = None
# Iterate over each node in the connected component until we find a node with degree=1
for node in cc:
if cover_graph.degree[node] == 1:
current_node = node
break
assert current_node is not None
# Starting with the degree=1 node, build the AGP object from nodes in the path.
visited_nodes = {current_node}
degree = 0
obj_id = 1
obj_pos = 0
# Traverse the component until we find the other end node
while degree != 1:
conn_nodes = set(cover_graph.neighbors(current_node))
next_node = (conn_nodes - visited_nodes).pop()
degree = cover_graph.degree[next_node]
comp_len = scaffold_graph.get_component_len(next_node[:-2])
# Check if this is an intra or inter sequence edge
orientation = "+"
if next_node[:-2] == current_node[:-2]:
if next_node.endswith("_b"):
orientation = "-"
assert current_node.endswith("_e")
agp.add_seq_line(
obj_header,
str(obj_pos + 1),
str(obj_pos + comp_len),
str(obj_id),
"W",
next_node[:-2],
"1",
str(comp_len),
orientation
)
obj_pos += comp_len
placed_components.add(next_node[:-2])
else:
# Organize the gap info
adjacency_data = scaffold_graph[current_node][next_node]
# AGP Column 5
all_is_known_gap_size = adjacency_data["is_known_gap_size"]
comp_type = "N" if any(all_is_known_gap_size) else "U"
# AGP column 6b
gap_size = 100
all_gap_sizes = adjacency_data["gap_size"]
fltrd_gap_sizes = [all_gap_sizes[i] for i in range(len(all_gap_sizes)) if all_is_known_gap_size[i]]
if fltrd_gap_sizes:
if len(fltrd_gap_sizes) == 1:
gap_size = fltrd_gap_sizes[0]
else:
gap_size = get_gap_size(fltrd_gap_sizes, gap_func)
# AGP column 7b
all_gap_types = set(adjacency_data["gap_type"])
gap_type = "scaffold"
if len(all_gap_types) == 1:
gap_type = all_gap_types.pop()
# AGP column 8b
has_linkage = "yes" if any(adjacency_data["linkage"]) else "no"
# AGP column 9b
all_evidences = set(adjacency_data["linkage_evidence"])
linkage_evidence = "na"
if has_linkage == "yes":
if "na" in all_evidences:
all_evidences.remove("na")
linkage_evidence = ";".join([str(i) for i in all_evidences])
agp.add_gap_line(
obj_header,
str(obj_pos + 1),
str(obj_pos + gap_size),
str(obj_id),
comp_type,
str(gap_size),
gap_type,
has_linkage,
linkage_evidence
)
obj_pos += gap_size
obj_id += 1
visited_nodes.add(next_node)
current_node = next_node
# Write all unplaced contigs
remaining_components = scaffold_graph.components - placed_components
for c in remaining_components:
agp.add_seq_line(
c + "_RagTag" * add_suffix_to_unplaced,
"1",
str(scaffold_graph.get_component_len(c)),
"1",
"W",
c,
"1",
str(scaffold_graph.get_component_len(c)),
"+"
)
agp.write()
def main():
description = "Scaffold merging: derive a consensus scaffolding solution by reconciling distinct scaffoldings of " \
"'asm.fa'"
parser = argparse.ArgumentParser(description=description, usage="ragtag.py merge <asm.fa> <scf1.agp> <scf2.agp> [...]")
parser.add_argument("components", metavar="<asm.fasta>", nargs='?', default="", type=str, help="assembly fasta file (uncompressed or bgzipped)")
parser.add_argument("agps", metavar="<scf1.agp> <scf2.agp> [...]", nargs='*', default=[], type=str, help="scaffolding AGP files")
merge_options = parser.add_argument_group("merging options")
merge_options.add_argument("-f", metavar="FILE", default="", type=str, help="CSV list of (AGP file,weight) [null]")
merge_options.add_argument("-j", metavar="<skip.txt>", type=str, default="", help="list of query headers to leave unplaced [null]")
merge_options.add_argument("-l", metavar="INT", default=100000, type=int, help="minimum assembly sequence length [100000]")
merge_options.add_argument("-e", metavar="FLOAT", default=0.0, type=float, help="minimum edge weight. NA if using Hi-C [0.0]")
merge_options.add_argument("--gap-func", metavar="STR", default="min", type=str, help="function for merging gap lengths {'min', 'max', or 'mean'} [min]")
io_options = parser.add_argument_group("input/output options")
io_options.add_argument("-o", metavar="PATH", type=str, default="ragtag_output", help="output directory [./ragtag_output]")
io_options.add_argument("-w", action='store_true', default=False, help="overwrite intermediate files")
io_options.add_argument("-u", action='store_true', default=False, help="add suffix to unplaced sequence headers")
io_options.add_argument("--debug", action='store_true', default=False, help=argparse.SUPPRESS)
hic_options = parser.add_argument_group("Hi-C options")
hic_options.add_argument("-b", metavar="FILE", default="", type=str, help="Hi-C alignments in BAM format, sorted by read name [null]")
hic_options.add_argument("-r", metavar="STR", default="GATC", type=str, help="CSV list of restriction enzymes/sites or 'DNase' [GATC]")
hic_options.add_argument("-p", metavar="FLOAT", default=1.0, type=float, help="portion of the sequence termini to consider for links [1.0]")
hic_options.add_argument("--list-enzymes", action='store_true', default=False, help="list all available restriction enzymes/sites")
args = parser.parse_args()
# Print a restriction enzyme help message if requested
if args.list_enzymes:
RestrictionEnzymes.get_info()
sys.exit(0)
if not args.components:
parser.print_help()
sys.exit("\n** The assembly FASTA file is required **")
if not args.agps and not args.f:
parser.print_help()
sys.exit("\n** At least two AGP files are required **")
log("VERSION", "RagTag " + get_ragtag_version())
log("WARNING", "This is a beta version of `ragtag merge`")
log("CMD", "ragtag.py merge " + " ".join(sys.argv[1:]))
# Check that the components FASTA file exists
comp_fname = args.components
if not os.path.isfile(comp_fname):
raise ValueError("Could not find file: %s" % comp_fname)
# Optional arguments
agp_fofn = args.f
hic_bam_fname = args.b
re_string = args.r
portion = args.p
# Set the minimum component sequence length
min_comp_len = args.l
if min_comp_len < 0:
min_comp_len = 0
# Set the minimum edge weight
min_edge_weight = args.e
if min_edge_weight < 0:
min_edge_weight = 0
# Set the gap merging function options
gap_func = args.gap_func.upper()
if gap_func not in {"MIN", "MAX", "MEAN"}:
raise ValueError("Gap merging function must be either 'min', 'max', or 'mean'. Got: {}".format(args.gap_func))
# Debugging options
debug_mode = args.debug
# I/O options
output_path = args.o
if not os.path.isdir(output_path):
os.mkdir(output_path)
output_path = os.path.abspath(output_path) + "/"
file_prefix = "ragtag.merge"
overwrite_files = args.w
add_suffix = args.u
if not add_suffix:
log("WARNING", "Without '-u' invoked, some component/object AGP pairs might share the same ID. Some external programs/databases don't like this. To ensure valid AGP format, use '-u'.")
# get the set of contigs to skip
comp_exclusion_set = set()
skip_fname = args.j
if skip_fname:
skip_fname = os.path.abspath(skip_fname)
with open(skip_fname, "r") as f:
for line in f:
comp_exclusion_set.add(line.rstrip().split()[0])
# Setup a file for general logging
merge_log = output_path + file_prefix + ".err"
open(merge_log, "w").close() # Wipe the log file
# Process the AGP files
agp_list = [os.path.abspath(i) for i in args.agps]
weight_list = [1 for _ in range(len(agp_list))]
# Check for file of AGPs and weights
if agp_fofn:
agp_list, weight_list = [], []
with open(agp_fofn, "r") as f:
for line in f:
fields = line.rstrip().split(",")
agp_list.append(fields[0])
weight_list.append(float(fields[1]))
if len(agp_list) < 2:
raise ValueError("At least two AGP files are required for merging")
# Build the graph and filter nodes by sequence length
log("INFO", "Building the scaffold graph from the AGP files")
agp_multi_sg = AGPMultiScaffoldGraph(comp_fname)
agp_multi_sg.add_agps(agp_list, in_weights=weight_list, exclusion_set=comp_exclusion_set)
if min_comp_len:
agp_multi_sg.filter_by_seq_len(min_comp_len)
if debug_mode:
nx.readwrite.gml.write_gml(agp_multi_sg.graph, output_path + "ragtag.merge.msg.gml")
# Merge the SAG
log("INFO", "Merging the scaffold graph")
agp_sg = agp_multi_sg.merge()
# Check if we are using Hi-C links to weight the graph.
if hic_bam_fname:
log("INFO", "Weighting the scaffold graph with Hi-C links")
if not comp_fname or not re_string:
raise RuntimeError("Hi-C requires alignments (-b) assembly sequences (-a) and restriction sites (-r)")
cmd = [
"ragtag_create_links.py",
"-a", comp_fname,
"-b", hic_bam_fname,
"-r", re_string,
"-p", str(portion)
]
out_links_fname = output_path + file_prefix + ".links"
if os.path.isfile(out_links_fname):
if not overwrite_files:
log("INFO", "Retaining pre-existing file: " + out_links_fname)
else:
run_oae(cmd, out_links_fname, merge_log)
else:
run_oae(cmd, out_links_fname, merge_log)
hic_sg = build_hic_graph(out_links_fname, comp_fname)
agp_sg = agp_sg.steal_weights_from(hic_sg)
# Filter by edge weight
if min_edge_weight and not hic_bam_fname:
agp_sg.filter_by_weight(min_edge_weight)
if debug_mode:
agp_sg.connect_and_write_gml(output_path + file_prefix + ".sg.gml")
# Compute a solution to the ScaffoldGraph
log("INFO", "Computing a scaffolding solution")
cover_graph = get_maximal_matching(agp_sg)
if debug_mode:
tmp_cover_graph = nx.Graph()
for u, v in cover_graph.edges:
tmp_cover_graph.add_edge(u, v)
nx.readwrite.gml.write_gml(tmp_cover_graph, output_path + file_prefix + ".covergraph.gml")
# Write the scaffolding output to an AGP file
log("INFO", "Writing results")
write_agp_solution(cover_graph, agp_sg, output_path + file_prefix + ".agp", gap_func=gap_func, add_suffix_to_unplaced=add_suffix)
# Generate a FASTA file corresponding to the AGP
cmd = [
"ragtag_agp2fa.py",
output_path + file_prefix + ".agp",
comp_fname
]
run_oae(cmd, output_path + file_prefix + ".fasta", merge_log)
log("INFO", "Goodbye")
if __name__ == "__main__":
main()