Repository navigation
Expand file tree
/
Copy pathMinia.cpp
More file actions
326 lines (258 loc) · 14.8 KB
/
Copy pathMinia.cpp
File metadata and controls
326 lines (258 loc) · 14.8 KB
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
/*****************************************************************************
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 INRIA
* Authors: R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/********************************************************************************/
// We include required definitions
/********************************************************************************/
#include <Minia.hpp>
#include <gatb/debruijn/impl/Simplifications.hpp>
#include <gatb/debruijn/impl/GraphUnitigs.hpp>
#include <fstream>
#include <iomanip> // for setprecision
using namespace std;
/********************************************************************************/
#define DEBUG(a) //a
/********************************************************************************/
static const char* STR_TRAVERSAL_KIND = "-traversal";
static const char* STR_FASTA_LINE_SIZE = "-fasta-line";
static const char* STR_KEEP_ISOLATED = "-keep-isolated";
static const char* progressFormat0 = "Minia : assembly";
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
Minia::Minia () : Tool ("minia")
{
#ifdef GIT_SHA1
std::cout << "Minia 3, git commit " << GIT_SHA1 << std::endl;
#endif
// reinit the parser to get rid of options added by the Tool class, as we'll add them again in the Graph parser
setParser (new OptionsParser ("minia"));
/** We add options specific to Minia (most important at the end). */
OptionsParser* assemblyParser = new OptionsParser ("assembly");
assemblyParser->push_front (new OptionOneParam (STR_FASTA_LINE_SIZE, "number of nucleotides per line in fasta output (0 means one line)", false, "0"));
assemblyParser->push_front (new OptionOneParam (STR_TRAVERSAL_KIND, "traversal type ('contig', 'unitig')", false, "contig" ));
assemblyParser->push_front (new OptionNoParam (STR_KEEP_ISOLATED, "keep short (<= max(2k, 150 bp)) isolated output sequences", false));
assemblyParser->push_front (new OptionOneParam (STR_URI_INPUT, "input reads (fasta/fastq/compressed) or hdf5 file", false));
getParser()->push_back (assemblyParser);
OptionsParser* simplificationsParser = new OptionsParser ("graph simplifications");
// this requires that Minia is compiled to support kmer values of 32 at least.
Simplifications<GraphUnitigsTemplate<32>,NodeGU,EdgeGU> graphSimplifications(nullptr, 1, false); // get a graph simplifications object just to get default parameters
simplificationsParser->push_back (new OptionNoParam ("-no-bulge-removal", "ask to not perform bulge removal", false));
simplificationsParser->push_back (new OptionNoParam ("-no-tip-removal", "ask to not perform tip removal", false));
simplificationsParser->push_back (new OptionNoParam ("-no-ec-removal", "ask to not perform erroneous connection removal", false));
simplificationsParser->push_back (new OptionOneParam ("-tip-len-topo-kmult", "remove all tips of length <= k * X bp", false, to_string(graphSimplifications._tipLen_Topo_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-tip-len-rctc-kmult", "remove tips that pass coverage criteria, of length <= k * X bp", false, to_string(graphSimplifications._tipLen_RCTC_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-tip-rctc-cutoff", "tip relative coverage coefficient: mean coverage of neighbors > X * tip coverage", false, to_string(graphSimplifications._tipRCTCcutoff)));
simplificationsParser->push_back (new OptionOneParam ("-bulge-len-kmult", "bulges shorter than k*X bp are candidate to be removed", false, to_string(graphSimplifications._bulgeLen_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-bulge-len-kadd", "bulges shorter than k+X bp are candidate to be removed", false, to_string(graphSimplifications._bulgeLen_kAdd)));
simplificationsParser->push_back (new OptionOneParam ("-bulge-altpath-kadd", "explore up to k+X nodes to find alternative path", false, to_string(graphSimplifications._bulgeAltPath_kAdd))); // TODO k should not appear in that equation
simplificationsParser->push_back (new OptionOneParam ("-bulge-altpath-covmult", "bulges of coverage <= X*cov_altpath will be removed", false, to_string(graphSimplifications._bulgeAltPath_covMult)));
simplificationsParser->push_back (new OptionOneParam ("-ec-len-kmult", "EC shorter than k*X bp are candidates to be removed", false, to_string(graphSimplifications._ecLen_kMult)));
simplificationsParser->push_back (new OptionOneParam ("-ec-rctc-cutoff", "EC relative coverage coefficient (similar in spirit as tip)", false, to_string(graphSimplifications._ecRCTCcutoff)));
getParser()->push_back (simplificationsParser);
// when we input reads, dbgh5 is executed, so its options are needed here
IOptionsParser* graphParser = Graph::getOptionsParser(false);
// we hide the STR_URI_INPUT option, otherwise we would have it twice
if (IOptionsParser* p = graphParser->getParser(STR_URI_INPUT)) { p->setVisible(false); }
// we set the default value for the abundance min (2)
if (Option* p = dynamic_cast<Option*> (graphParser->getParser(STR_KMER_ABUNDANCE_MIN))) { p->setDefaultValue ("2"); }
// through an undocumented environment variable, we can set the temporary path (useful to not have to specify -out-tmp every time)
char *hidden_env_variable_out_tmp = std::getenv("MINIA_OUT_TMP");
if (hidden_env_variable_out_tmp)
{
if (Option* p = dynamic_cast<Option*> (graphParser->getParser(STR_URI_OUTPUT_TMP))) { p->setDefaultValue ((string)hidden_env_variable_out_tmp); }
}
getParser()->push_back(graphParser, 1);
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
struct Parameter
{
Parameter (Minia& minia) : minia(minia){}
Minia& minia;
};
template<size_t span>
struct MiniaFunctor { void operator () (Parameter parameter)
{
Minia& minia = parameter.minia;
// selection of type of graph is done HERE
//typedef GraphTemplate<NodeFast<span>,EdgeFast<span>,GraphDataVariantFast<span>> GraphType;
typedef GraphUnitigsTemplate<span> GraphType;
GraphType graph;
{
TIME_INFO (minia.getTimeInfo(), "graph construction");
if (minia.getInput()->get(STR_URI_INPUT) != 0)
{
graph = GraphType::create (minia.getInput());
}
else
{
throw OptionFailure (minia.getParser(), "Specifiy -in");
}
}
/** We build the contigs. */
string output = minia.assemble<GraphType, NodeGU, EdgeGU, span>(graph);
// link contigs
uint nb_threads = 1; // doesn't matter because for now link_tigs is single-threaded
bool verbose = true;
link_tigs<span>(output, minia.k, nb_threads, minia.nbContigs, verbose, false);
/** We gather some statistics. */
minia.getInfo()->add (1, minia.getTimeInfo().getProperties("time"));
}
};
void Minia::execute ()
{
/** we get the kmer size chosen by the end user. */
k = getInput()->getInt (STR_KMER_SIZE);
/** We launch Minia with the correct Integer implementation according to the choosen kmer size. */
Integer::apply<MiniaFunctor,Parameter> (k, Parameter (*this));
}
template <typename Graph_type, typename Node, typename Edge, size_t span>
void Minia::assembleFrom(Node startingNode, Graph_type& graph, IBank *outputBank)
{
unsigned int isolatedCutoff = std::max(2*(unsigned int)graph.getKmerSize(), (unsigned int)150);
bool isolatedLeft, isolatedRight;
float coverage = 0;
string sequence = graph.simplePathBothDirections(startingNode, isolatedLeft, isolatedRight, true, coverage);
Sequence seq (Data::ASCII);
seq.getData().setRef ((char*)sequence.c_str(), sequence.size());
/** We set the sequence comment. */
stringstream ss1;
// spades-like header (compatible with bandage)
//ss1 << "NODE_"<< nbContigs + 1 << "_length_" << sequence.size() << "_cov_" << fixed << std::setprecision(3) << coverage << "_ID_" << nbContigs;
// bcalm-like header (that can be converted to GFA)
ss1 << nbContigs << " LN:i:" << sequence.size() << " KC:i:" << (unsigned int)(coverage*(sequence.size()-k+1)) << " km:f:" << fixed << std::setprecision(3) << coverage ;
seq._comment = ss1.str();
unsigned int lenTotal = sequence.size();
if (lenTotal > isolatedCutoff || (lenTotal <= isolatedCutoff && (!(isolatedLeft && isolatedRight))) || keepIsolatedTigs)
{
outputBank->insert (seq);
nbContigs += 1;
totalNt += lenTotal;
if (lenTotal > maxContigLen) { maxContigLen = lenTotal; }
}
else
nbSmallContigs++;
return;
}
/*********************************************************************
** METHOD :
** PURPOSE :
** INPUT :
** OUTPUT :
** RETURN :
** REMARKS :
*********************************************************************/
template <typename Graph_type, typename Node, typename Edge, size_t span>
string Minia::assemble (/*const, removed because Simplifications isn't const anymore*/ Graph_type& graph)
{
TIME_INFO (getTimeInfo(), "assembly");
string output = (getInput()->get(STR_URI_OUTPUT) ?
getInput()->getStr(STR_URI_OUTPUT) :
System::file().getBaseName (getInput()->getStr(STR_URI_INPUT))
)+ ".contigs.fa";
/** We create the output bank. Note that we could make this a little bit prettier
* => possibility to save the contigs in specific output format (other than fasta). */
IBank* outputBank = new BankFasta (output);
LOCAL (outputBank);
/** We set the fasta line size. */
BankFasta::setDataLineSize (getInput()->getInt (STR_FASTA_LINE_SIZE));
bool simplifyGraph = false;
string traversalKind = "unitig"; // we output unitigs of the simplified graph or the original graph
simplifyGraph = getInput()->getStr(STR_TRAVERSAL_KIND).compare("contig") == 0;
nbContigs = 0;
nbSmallContigs = 0;
totalNt = 0;
maxContigLen = 0;
keepIsolatedTigs = getParser()->saw(STR_KEEP_ISOLATED);
string str_tipRemoval = "", str_bubbleRemoval = "", str_ECRemoval = "";
/** We get an iterator over all nodes . */
ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> itNode (graph.Graph_type::iterator(), progressFormat0);
// if we want unitigs, then don't simplify the graph; else do it
if (simplifyGraph)
{
int nbCores = getInput()->getInt(STR_NB_CORES);
bool verbose=false;
Simplifications<Graph_type,Node,Edge> graphSimplifications(&graph, nbCores, verbose);
if (getParser()->saw("-no-tip-removal"))
graphSimplifications._doTipRemoval = false;
if (getParser()->saw("-no-bulge-removal"))
graphSimplifications._doBulgeRemoval = false;
if (getParser()->saw("-no-ec-removal"))
graphSimplifications._doECRemoval = false;
if (getParser()->saw("-tip-len-topo-kmult"))
graphSimplifications._tipLen_Topo_kMult = getInput()->getDouble("-tip-len-topo-kmult");
if (getParser()->saw("-tip-len-rctc-kmult"))
graphSimplifications._tipLen_RCTC_kMult = getInput()->getDouble("-tip-len-rctc-kmult");
if (getParser()->saw("-tip-rctc-cutoff"))
graphSimplifications._tipRCTCcutoff = getInput()->getDouble("-tip-rctc-cutoff");
if (getParser()->saw("-bulge-len-kmult"))
graphSimplifications._bulgeLen_kMult = getInput()->getDouble("-bulge-len-kmult");
if (getParser()->saw("-bulge-len-kadd"))
graphSimplifications._bulgeLen_kAdd = getInput()->getDouble("-bulge-len-kadd");
if (getParser()->saw("-bulge-altpath-kadd"))
graphSimplifications._bulgeAltPath_kAdd = getInput()->getDouble("-bulge-altpath-kadd");
if (getParser()->saw("-bulge-altpath-covmult"))
graphSimplifications._bulgeAltPath_covMult = getInput()->getDouble("-bulge-altpath-covmult");
if (getParser()->saw("-ec-len-kmult"))
graphSimplifications._ecLen_kMult = getInput()->getDouble("-ec-len-kmult");
if (getParser()->saw("-ec-rctc-cutoff"))
graphSimplifications._ecRCTCcutoff = getInput()->getDouble("-ec-rctc-cutoff");
graphSimplifications.simplify();
str_tipRemoval = graphSimplifications.tipRemoval;
str_bubbleRemoval = graphSimplifications.bubbleRemoval;
str_ECRemoval = graphSimplifications.ECRemoval;
}
//graph.debugPrintAllUnitigs(); // debugging
/** We loop over all nodes. */
for (itNode.first(); !itNode.isDone(); itNode.next())
{
Node node = itNode.item();
if (graph.unitigIsMarked(node)) { continue; }
if (graph.isNodeDeleted(node)) { continue; }
DEBUG ((cout << endl << "-------------------------- " << graph.toString (node) << " -------------------------" << endl));
assembleFrom<Graph_type, Node, Edge, span>(node, graph, outputBank);
}
/** We add the input parameters to the global properties. */
getInfo()->add (1, getInput());
/** We gather some statistics. */
getInfo()->add (1, "stats");
getInfo()->add (2, "traversal", "%s", getInput()->getStr(STR_TRAVERSAL_KIND).c_str());
getInfo()->add (2, "nb_solid_kmers", "%d", graph._nbSolidKmers);
getInfo()->add (2, "nb_contigs", "%d", nbContigs);
getInfo()->add (2, "nb_small_contigs_discarded","%d", nbSmallContigs);
getInfo()->add (2, "nt_assembled", "%ld", totalNt);
getInfo()->add (2, "max_length", "%d", maxContigLen);
getInfo()->add (2, "graph simpification stats");
getInfo()->add (3, "tips removed", "%s", str_tipRemoval.c_str());
getInfo()->add (3, "bulges removed", "%s", str_bubbleRemoval.c_str());
getInfo()->add (3, "EC removed", "%s", str_ECRemoval.c_str());
getInfo()->add (2, "assembly traversal stats");
return output;
}