utils/deadzones.cpp at master · smithlabcode/utils · GitHub

History

432 lines (379 loc) · 13.9 KB

Raw

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

431

432

/* deadzones: A program for identifying genomic deadzones

* Andrew D. Smith

* Authors: Andrew D. Smith

* This program is free software: you can redistribute it and/or modify

* it under the terms of the GNU 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 General Public License for more details.

* You should have received a copy of the GNU General Public License

* along with this program. If not, see <http://www.gnu.org/licenses/>.

#include "smithlab_utils.hpp"

#include "GenomicRegion.hpp"

#include "OptionParser.hpp"

#include <numeric>

#include <cmath>

#if defined(_OPENMP)

#include <parallel/algorithm>

#else

#include <algorithm>

#endif

#include <tr1/unordered_map>

using std::tr1::unordered_map;

using std::string;

using std::vector;

using std::cout;

using std::endl;

using std::cerr;

class IndexLess {

public:

IndexLess(const size_t k, const string &s) :

kmer(k), itr(s.begin()) {}

bool operator()(size_t a, size_t b) const {

const string::const_iterator lim(itr + a + kmer);

string::const_iterator a_itr(itr + a), b_itr(itr + b);

while (a_itr < lim && *(a_itr) == *(b_itr)) {

++a_itr; ++b_itr;

}

return (*a_itr < *b_itr && a_itr < lim);

}

private:

size_t kmer;

const string::const_iterator itr;

};

template <class In> bool

lexico_equal(In first, In last, In first2) {

while (first != last)

if (*first++ != *first2++) return false;

return true;

}

static void

sort_index(const bool VERBOSE, const size_t kmer, const string &prefix,

const string &seq, vector<size_t> &ambigs,

const unordered_map<size_t, size_t> &invalid_pool) {

if (VERBOSE) cerr << "[BUILDING INDEX] ";

vector<size_t> index;

const string::const_iterator lim(seq.end() - kmer + 1);

for (string::const_iterator j = seq.begin(); j != lim; ++j)

if ((lexico_equal(prefix.begin(), prefix.end(), j)) &&

(!(invalid_pool.find(j - seq.begin()) != invalid_pool.end())))

index.push_back(j - seq.begin());

if (!index.empty()) {

if (VERBOSE) cerr << "[SORTING INDEX] ";

IndexLess index_less(kmer, seq);

#if defined(_OPENMP)

__gnu_parallel::sort(index.begin(), index.end(), index_less);

#else

sort(index.begin(), index.end(), index_less);

#endif

if (VERBOSE) cerr << "[FINDING DEADS] ";

const size_t len = seq.length();

const string::const_iterator start(seq.begin());

const string::const_iterator end(start + kmer);

size_t prev = index.front();

bool prev_inserted = false;

for (size_t i = 1; i < index.size(); ++i) {

const size_t curr = index[i];

if (lexico_equal(start + prev, end + prev, start + curr) &&

prev + curr != len) {

if (!prev_inserted)

ambigs.push_back(prev);

ambigs.push_back(curr);

prev_inserted = true;

}

else prev_inserted = false;

prev = curr;

}

else if (VERBOSE) cerr << "[EMPTY INDEX] ";

}

static void

sort_index(const bool VERBOSE, const bool BISULFITE,

const bool AG_WILDCARD,

const size_t kmer, const size_t prefix_len,

const string &seq, vector<size_t> &ambigs,

const unordered_map<size_t, size_t> &invalid_pool) {

static const float DENOM = CLOCKS_PER_SEC;

const size_t n_prefix =

static_cast<size_t>(pow(smithlab::alphabet_size, prefix_len));

for (size_t i = 0; i < n_prefix; ++i) {

const string prefix(i2mer(prefix_len, i));

if (!BISULFITE ||

((!AG_WILDCARD && prefix.find('C') == string::npos) ||

(AG_WILDCARD && prefix.find('G') == string::npos))) {

const clock_t start(clock());

if (VERBOSE) cerr << "[PREFIX=" << prefix << "] ";

sort_index(VERBOSE, kmer, prefix, seq, ambigs, invalid_pool);

const clock_t end(clock());

if (VERBOSE)

cerr << "[" << (end - start)/DENOM << " SEC] [DONE]" << endl;

}

static void

write_dead(std::ofstream &out, const string &chrom_name,

const char strand, vector<size_t>::const_iterator curr,

const vector<size_t>::const_iterator lim) {

assert(curr <= lim);

size_t prev_ambig = *curr;

++curr;

for (; curr < lim; ++curr)

if (*curr - 1 != *(curr - 1)) {

out << GenomicRegion(chrom_name, prev_ambig,

*(curr - 1) + 1, "X", 0, strand) << endl;

prev_ambig = *curr;

}

out << GenomicRegion(chrom_name, prev_ambig,

*(curr - 1) + 1, "X", 0, strand) << endl;

}

static void

get_dead(const bool VERBOSE, const string &outfile, const size_t kmer,

const vector<size_t> &seqoffsets, const vector<string> &chrom_names,

vector<size_t> &ambigs) {

const size_t max_offset = seqoffsets.back();

for (size_t i = 0; i < ambigs.size(); ++i) {

if (ambigs[i] >= max_offset)

ambigs[i] = 2*max_offset - ambigs[i] - kmer;

assert(ambigs[i] < max_offset);

}

sort(ambigs.begin(), ambigs.end());

ambigs.erase(std::unique(ambigs.begin(), ambigs.end()), ambigs.end());

vector<size_t> offset_idx;

size_t n_ambigs = ambigs.size();

for (size_t i = 0, j = 0; i < seqoffsets.size() && j < n_ambigs; ++i) {

while (j < n_ambigs && ambigs[j] < seqoffsets[i]) ++j;

offset_idx.push_back(j);

}

size_t total_length = 0;

n_ambigs = ambigs.size();

for (size_t i = 0, prev_idx = 0; i < offset_idx.size(); ++i) {

for (size_t j = prev_idx; j < offset_idx[i]; ++j) {

assert(j < n_ambigs);

ambigs[j] -= total_length;

}

prev_idx = offset_idx[i];

total_length = seqoffsets[i];

}

std::ofstream out(outfile.c_str());

for (size_t i = 0, prev_idx = 0; i < offset_idx.size(); ++i) {

write_dead(out, chrom_names[i], '+', ambigs.begin() +

prev_idx, ambigs.begin() + offset_idx[i]);

prev_idx = offset_idx[i];

}

out.close();

}

static void

get_dead_bs(const bool VERBOSE, const string &outfile, const size_t kmer,

const vector<size_t> &seqoffsets, const vector<string> &chrom_names,

vector<size_t> &ambigs) {

assert(!ambigs.empty());

sort(ambigs.begin(), ambigs.end());

const size_t max_offset = seqoffsets.back();

if (VERBOSE)

cerr << "[PREPARING POS-STRAND BS DEADS]" << endl;

// Do the positive strand bisulfite deadzones

const size_t lim = lower_bound(ambigs.begin(), ambigs.end(),

max_offset) - ambigs.begin();

// make a partition vector of the offsets, the last being "lim"

vector<size_t> offset_idx;

size_t n_ambigs = ambigs.size();

for (size_t i = 0, j = 0; i < seqoffsets.size() && j < n_ambigs; ++i) {

while (j < n_ambigs && ambigs[j] < seqoffsets[i]) ++j;

offset_idx.push_back(j);

}

size_t total_length = 0;

for (size_t i = 0, prev_idx = 0; i < offset_idx.size(); ++i) {

for (size_t j = prev_idx; j < offset_idx[i]; ++j)

ambigs[j] -= total_length;

prev_idx = offset_idx[i];

total_length = seqoffsets[i];

}

std::ofstream out(outfile.c_str());

for (size_t i = 0, prev_idx = 0; i < offset_idx.size(); ++i) {

write_dead(out, chrom_names[i], '+', ambigs.begin() +

prev_idx, ambigs.begin() + offset_idx[i]);

prev_idx = offset_idx[i];

}

if (VERBOSE)

cerr << "[PREPARING NEG-STRAND BS DEADS]" << endl;

// Move the negative strand deadzones into the first portion of the

// vector and correct their indexes.

for (size_t j = 0, i = lim; i < ambigs.size(); ++i)

ambigs[j++] = 2*max_offset - ambigs[i] - kmer;

ambigs.erase(ambigs.end() - lim, ambigs.end());

reverse(ambigs.begin(), ambigs.end());

offset_idx.clear();

n_ambigs = ambigs.size();

for (size_t i = 0, j = 0; i < seqoffsets.size() && j < n_ambigs; ++i) {

while (j < n_ambigs && ambigs[j] < seqoffsets[i]) ++j;

offset_idx.push_back(j);

}

total_length = 0;

for (size_t i = 0, prev_idx = 0; i < offset_idx.size(); ++i) {

for (size_t j = prev_idx; j < offset_idx[i]; ++j)

ambigs[j] -= total_length;

prev_idx = offset_idx[i];

total_length = seqoffsets[i];

}

for (size_t i = 0, prev_idx = 0; i < offset_idx.size(); ++i) {

write_dead(out, chrom_names[i], '-', ambigs.begin() +

prev_idx, ambigs.begin() + offset_idx[i]);

prev_idx = offset_idx[i];

}

out.close();

}

// This function appends the reverse complement in a space efficient way

static void

append_revcomp(string &long_seq) {

const size_t seqlen = long_seq.length();

long_seq.resize(2*seqlen);

copy(long_seq.begin(), long_seq.begin() + seqlen, long_seq.begin() + seqlen);

revcomp_inplace(long_seq.begin() + seqlen, long_seq.end());

}

static void

identify_chromosomes(const bool VERBOSE,

const string fasta_suffix,

const string chrom_file,

vector<string> &chrom_files) {

if (VERBOSE)

cerr << "[IDENTIFYING CHROMS] ";

if (isdir(chrom_file.c_str()))

read_dir(chrom_file, fasta_suffix, chrom_files);

else chrom_files.push_back(chrom_file);

if (VERBOSE) {

cerr << "[DONE]" << endl

<< "chromosome files found (approx size):" << endl;

for (vector<string>::const_iterator i = chrom_files.begin();

i != chrom_files.end(); ++i)

cerr << *i << " (" << roundf(get_filesize(*i)/1e06) << "Mbp)" << endl;

cerr << endl;

}

int

main(int argc, const char **argv) {

try {

// Parameter variables

size_t kmer = 0;

size_t prefix_len = 0;

string outfile;

string fasta_suffix = "fa";

bool VERBOSE = false;

bool BISULFITE = false;

bool AG_WILDCARD = false;

/****************** COMMAND LINE OPTIONS ********************/

OptionParser opt_parse("deadzones", "program for finding deadzones",

"<1-or-more-FASTA-chrom-files>");

opt_parse.add_opt("output", 'o', "Name of output file (default: stdout)",

true, outfile);

opt_parse.add_opt("kmer", 'k', "Width of k-mers", true, kmer);

opt_parse.add_opt("prefix", 'p', "prefix length", true, prefix_len);

opt_parse.add_opt("bisulfite", 'B', "get bisulfite deadzones",

false, BISULFITE);

opt_parse.add_opt("ag-wild", 'A', "A/G wildcard for bisulfite",

false, AG_WILDCARD);

opt_parse.add_opt("suffix", 's', "suffix of FASTA files "

"(assumes -c indicates dir)", false , fasta_suffix);

opt_parse.add_opt("verbose", 'v', "print more run information",

false, VERBOSE);

vector<string> leftover_args;

opt_parse.parse(argc, argv, leftover_args);

if (argc == 1 || opt_parse.help_requested()) {

cerr << opt_parse.help_message() << endl;

return EXIT_SUCCESS;

}

if (opt_parse.about_requested()) {

cerr << opt_parse.about_message() << endl;

return EXIT_SUCCESS;

}

if (opt_parse.option_missing()) {

cerr << opt_parse.option_missing_message() << endl;

return EXIT_SUCCESS;

}

if (leftover_args.empty()) {

cerr << opt_parse.help_message() << endl;

return EXIT_SUCCESS;

}

const string chrom_file = leftover_args.front();

/****************** END COMMAND LINE OPTIONS *****************/

vector<string> seqfiles;

identify_chromosomes(VERBOSE, fasta_suffix, chrom_file, seqfiles);

string long_seq;

vector<size_t> seqoffsets;

vector<string> chrom_names;

if (VERBOSE)

cerr << "[READING SEQUENCE FILES]" << endl;

for (size_t i = 0; i < seqfiles.size(); ++i) {

if (isdir(seqfiles[i].c_str()))

throw SMITHLABException("\"" + seqfiles[i] +

"\" not a FASTA format sequence file?");

vector<string> names, sequences;

read_fasta_file(seqfiles[i].c_str(), names, sequences);

for (size_t j = 0; j < sequences.size(); ++j) {

long_seq += sequences[j];

seqoffsets.push_back(long_seq.length());

chrom_names.push_back(names[j]);

}

if (VERBOSE)

cerr << seqfiles[i] << "\t(SEQS: " << names.size() << ")" << endl;

}

transform(long_seq.begin(), long_seq.end(), long_seq.begin(),

std::ptr_fun(&::toupper));

if (VERBOSE)

cerr << "[PREPARING CONCATENATED SEQUENCE]" << endl;

append_revcomp(long_seq);

if (BISULFITE) {

if (AG_WILDCARD)

replace(long_seq.begin(), long_seq.end(), 'G', 'A');

else

replace(long_seq.begin(), long_seq.end(), 'C', 'T');

}

if (VERBOSE)

cerr << "[PREPARING INVALID INDEXES]" << endl;

unordered_map<size_t, size_t> invalid_pool;

size_t max = seqoffsets[seqoffsets.size()-1];

for (size_t i = 0; i < seqoffsets.size(); i++)

{ for (size_t j=seqoffsets[i]-kmer+1; j<=seqoffsets[i]-1; j++)

invalid_pool[j] = 1;

for (size_t j=max+(max-seqoffsets[i])-kmer+1; j<=max+(max-seqoffsets[i]-1); j++)

invalid_pool[j] = 1;

}

if (VERBOSE)

cerr << "[IDENTIFYING AMBIGUOUS INDEXES]" << endl;

vector<size_t> ambigs;

sort_index(VERBOSE, BISULFITE, AG_WILDCARD, kmer, prefix_len, long_seq, ambigs, invalid_pool);

long_seq.clear();

if (ambigs.empty()) {

if (VERBOSE) cerr << "[NO DEADZONES FOUND]" << endl;

}

else {

if (BISULFITE) {

if (VERBOSE)

cerr << "[PREPARING BS DEADZONES]" << endl;

get_dead_bs(VERBOSE, outfile, kmer, seqoffsets, chrom_names, ambigs);

}

else {

if (VERBOSE)

cerr << "[PREPARING DEADZONES]" << endl;

get_dead(VERBOSE, outfile, kmer, seqoffsets, chrom_names, ambigs);

}

catch (SMITHLABException &e) {

cerr << "ERROR: " << e.what() << endl;

return EXIT_FAILURE;

}

catch (std::bad_alloc &ba) {

cerr << "ERROR: could not allocate memory" << endl;

return EXIT_FAILURE;

}

return EXIT_SUCCESS;

}

utils/deadzones.cpp at master · smithlabcode/utils · GitHub

Uh oh!

Expand file tree

Breadcrumbs

deadzones.cpp

Latest commit

History

Breadcrumbs

deadzones.cpp

File metadata and controls