| 1 |
#include "GBase.h" |
| 2 |
#include "GArgs.h" |
| 3 |
#include "GStr.h" |
| 4 |
#include "GList.hh" |
| 5 |
//#include "GXDropAlign.h" |
| 6 |
|
| 7 |
#define USAGE "Usage:\n\ |
| 8 |
seqalign -i <2line_file> | -a <seq1> -b <seq2>\n" |
| 9 |
|
| 10 |
bool debug=true; |
| 11 |
|
| 12 |
struct SEditScript{ |
| 13 |
uint32 *op; // array of edit operations |
| 14 |
uint32 size, num; // size of allocation, number in use |
| 15 |
uint32 last; // most recent operation added |
| 16 |
}; |
| 17 |
/* |
| 18 |
SEditScript *edit_script_free(SEditScript *es); |
| 19 |
SEditScript *edit_script_new(void); |
| 20 |
SEditScript *edit_script_append(SEditScript *es, SEditScript *et); |
| 21 |
*/ |
| 22 |
enum { |
| 23 |
EDIT_OP_MASK = 0x3, |
| 24 |
EDIT_OP_ERR = 0x0, |
| 25 |
EDIT_OP_INS = 0x1, |
| 26 |
EDIT_OP_DEL = 0x2, |
| 27 |
EDIT_OP_REP = 0x3 |
| 28 |
}; |
| 29 |
|
| 30 |
//enum { /* half of the (fixed) match score */ |
| 31 |
// ERROR_FRACTION=2, /* 1/this */ |
| 32 |
// MAX_SPACE=1000000, |
| 33 |
// sC = 0, sI = 1, sD = 2, LARGE=100000000 |
| 34 |
//}; |
| 35 |
|
| 36 |
#define ERROR_FRACTION 2 /* 1/this */ |
| 37 |
#define MAX_SPACE 1000000 |
| 38 |
#define LARGE 100000000 |
| 39 |
int sC = 0, sI = 1, sD = 2; |
| 40 |
|
| 41 |
uint32 edit_val_get(uint32 op) { |
| 42 |
return op >> 2; |
| 43 |
} |
| 44 |
uint32 edit_opc_get(uint32 op) { |
| 45 |
return op & EDIT_OP_MASK; |
| 46 |
} |
| 47 |
|
| 48 |
uint32 edit_op_cons(uint32 op, uint32 val) { |
| 49 |
return (val << 2) | (op & EDIT_OP_MASK); |
| 50 |
} |
| 51 |
|
| 52 |
uint32 edit_op_inc(uint32 op, uint32 n) { |
| 53 |
return edit_op_cons(edit_opc_get(op), edit_val_get(op) + n); |
| 54 |
} |
| 55 |
|
| 56 |
uint32 edit_op_inc_last(SEditScript *es, uint32 n) { |
| 57 |
uint32 *last; |
| 58 |
//ASSERT (es->num > 0); |
| 59 |
last = &(es->op[es->num-1]); |
| 60 |
*last = edit_op_inc(*last, n); |
| 61 |
return *last; |
| 62 |
} |
| 63 |
|
| 64 |
int edit_script_ready(SEditScript *es, uint32 n) { |
| 65 |
//uint32 *p; |
| 66 |
uint32 m = n + n/2; |
| 67 |
if (es->size <= n) { |
| 68 |
GREALLOC(es->op, m*sizeof(uint32)); |
| 69 |
//es->op = p; |
| 70 |
es->size = m; |
| 71 |
} |
| 72 |
return 1; |
| 73 |
} |
| 74 |
|
| 75 |
int edit_script_readyplus(SEditScript *es, uint32 n) { |
| 76 |
if (es->size - es->num <= n) |
| 77 |
return edit_script_ready(es, n + es->num); |
| 78 |
return 1; |
| 79 |
} |
| 80 |
|
| 81 |
int edit_script_put(SEditScript *es, uint32 op, uint32 n) { |
| 82 |
if (!edit_script_readyplus(es, 2)) |
| 83 |
return 0; |
| 84 |
es->last = op; |
| 85 |
//ASSERT(op != 0); |
| 86 |
es->op[es->num] = edit_op_cons(op, n); |
| 87 |
es->num += 1; |
| 88 |
es->op[es->num] = 0; /* sentinal */ |
| 89 |
|
| 90 |
return 1; |
| 91 |
} |
| 92 |
|
| 93 |
SEditScript *edit_script_init(SEditScript *es) { |
| 94 |
es->op = 0; |
| 95 |
es->size = es->num = 0; |
| 96 |
es->last = 0; |
| 97 |
edit_script_ready(es, 8); |
| 98 |
return es; |
| 99 |
} |
| 100 |
|
| 101 |
uint32 *edit_script_first(SEditScript *es) { |
| 102 |
return es->num > 0 ? &es->op[0] : 0; |
| 103 |
} |
| 104 |
|
| 105 |
uint32 *edit_script_next(SEditScript *es, uint32 *op) { |
| 106 |
// assumes flat address space ! |
| 107 |
if (&es->op[0] <= op && op < &es->op[es->num-1]) |
| 108 |
return op+1; |
| 109 |
else |
| 110 |
return 0; |
| 111 |
} |
| 112 |
|
| 113 |
static int edit_script_more(SEditScript *data, uint32 op, uint32 k) { |
| 114 |
if (op == EDIT_OP_ERR) { |
| 115 |
GError("edit_script_more: bad opcode %d:%d", op, k); |
| 116 |
return -1; |
| 117 |
} |
| 118 |
|
| 119 |
if (edit_opc_get(data->last) == op) |
| 120 |
edit_op_inc_last(data, k); |
| 121 |
else |
| 122 |
edit_script_put(data, op, k); |
| 123 |
|
| 124 |
return 0; |
| 125 |
} |
| 126 |
|
| 127 |
/* External */ |
| 128 |
SEditScript *edit_script_append(SEditScript *es, SEditScript *et) { |
| 129 |
uint32 *op; |
| 130 |
for (op = edit_script_first(et); op; op = edit_script_next(et, op)) |
| 131 |
edit_script_more(es, edit_opc_get(*op), edit_val_get(*op)); |
| 132 |
return es; |
| 133 |
} |
| 134 |
|
| 135 |
SEditScript *edit_script_new(void) { |
| 136 |
SEditScript *es = NULL; |
| 137 |
GCALLOC(es, sizeof(*es)); |
| 138 |
return edit_script_init(es); |
| 139 |
} |
| 140 |
|
| 141 |
SEditScript *edit_script_free(SEditScript *es) { |
| 142 |
if (es) { |
| 143 |
if (es->op) { |
| 144 |
//MemFree(es->op); |
| 145 |
GFREE(es->op); |
| 146 |
} |
| 147 |
//MemSet(es, 0, sizeof(*es)); |
| 148 |
//MemFree(es); |
| 149 |
GFREE(es); |
| 150 |
} |
| 151 |
return 0; |
| 152 |
} |
| 153 |
|
| 154 |
int edit_script_del(SEditScript *data, uint32 k) { |
| 155 |
return edit_script_more(data, EDIT_OP_DEL, k); |
| 156 |
} |
| 157 |
|
| 158 |
int edit_script_ins(SEditScript *data, uint32 k) { |
| 159 |
return edit_script_more(data, EDIT_OP_INS, k); |
| 160 |
} |
| 161 |
int edit_script_rep(SEditScript *data, uint32 k) { |
| 162 |
return edit_script_more(data, EDIT_OP_REP, k); |
| 163 |
} |
| 164 |
|
| 165 |
SEditScript *edit_script_reverse_inplace(SEditScript *es) { |
| 166 |
uint32 i; |
| 167 |
const uint32 num = es->num; |
| 168 |
const uint32 mid = num/2; |
| 169 |
const uint32 end = num-1; |
| 170 |
|
| 171 |
for (i = 0; i < mid; ++i) { |
| 172 |
const uint32 t = es->op[i]; |
| 173 |
es->op[i] = es->op[end-i]; |
| 174 |
es->op[end-i] = t; |
| 175 |
} |
| 176 |
return es; |
| 177 |
} |
| 178 |
|
| 179 |
/* ----- pool allocator ----- */ |
| 180 |
struct ThreeVal { |
| 181 |
int I, C, D; |
| 182 |
}; |
| 183 |
|
| 184 |
struct MBSpace { |
| 185 |
ThreeVal* space_array; |
| 186 |
int used, size; |
| 187 |
MBSpace *next; |
| 188 |
}; |
| 189 |
|
| 190 |
MBSpace* new_mb_space() { |
| 191 |
MBSpace* p; |
| 192 |
int amount; |
| 193 |
|
| 194 |
GMALLOC(p, sizeof(MBSpace)); |
| 195 |
amount = MAX_SPACE; |
| 196 |
GCALLOC(p->space_array, sizeof(ThreeVal)*amount); |
| 197 |
if (p->space_array == NULL) { |
| 198 |
GFREE(p); |
| 199 |
return NULL; |
| 200 |
} |
| 201 |
p->used = 0; |
| 202 |
p->size = amount; |
| 203 |
p->next = NULL; |
| 204 |
|
| 205 |
return p; |
| 206 |
} |
| 207 |
|
| 208 |
void refresh_mb_space(MBSpace* sp) |
| 209 |
{ |
| 210 |
while (sp) { |
| 211 |
sp->used = 0; |
| 212 |
sp = sp->next; |
| 213 |
} |
| 214 |
} |
| 215 |
|
| 216 |
void free_mb_space(MBSpace* sp) |
| 217 |
{ |
| 218 |
MBSpace* next_sp; |
| 219 |
while (sp) { |
| 220 |
next_sp = sp->next; |
| 221 |
//sp->space_array = MemFree(sp->space_array); |
| 222 |
GFREE(sp->space_array); |
| 223 |
//sp = MemFree(sp); |
| 224 |
GFREE(sp); |
| 225 |
sp = next_sp; |
| 226 |
} |
| 227 |
} |
| 228 |
|
| 229 |
ThreeVal* get_mb_space(MBSpace* S, int amount) |
| 230 |
{ |
| 231 |
ThreeVal* s; |
| 232 |
if (amount < 0) |
| 233 |
return NULL; |
| 234 |
|
| 235 |
while (S->used+amount > S->size) { |
| 236 |
if (S->next == NULL) |
| 237 |
if ((S->next = new_mb_space()) == NULL) { |
| 238 |
GError("Cannot get new space for greedy extension!\n"); |
| 239 |
return NULL; |
| 240 |
} |
| 241 |
S = S->next; |
| 242 |
} |
| 243 |
s = S->space_array+S->used; |
| 244 |
S->used += amount; |
| 245 |
return s; |
| 246 |
} |
| 247 |
|
| 248 |
struct GreedyAlignMem { |
| 249 |
int** flast_d; |
| 250 |
int* max_row_free; |
| 251 |
int* uplow_free; |
| 252 |
MBSpace* space; |
| 253 |
int max_d; |
| 254 |
GreedyAlignMem(int max_len, int reward, int penalty, int Xdrop) { |
| 255 |
flast_d=NULL; |
| 256 |
max_row_free=NULL; |
| 257 |
max_d=0; |
| 258 |
uplow_free=NULL; |
| 259 |
space=NULL; |
| 260 |
max_d = (int)(max_len / ERROR_FRACTION + 1); |
| 261 |
int d_diff = (Xdrop+reward/2)/(penalty+reward) + 1; |
| 262 |
//flast_d = (int**) malloc((max_d + 2) * sizeof(int)); |
| 263 |
GCALLOC(flast_d, (max_d+2)* sizeof(int)); |
| 264 |
if (flast_d == NULL) { |
| 265 |
GError("Error: cannot allocate GreedyAlignMem structure!\n"); |
| 266 |
} |
| 267 |
flast_d[0] = (int*)malloc((max_d + max_d + 6) * sizeof(int) * 2); |
| 268 |
if (flast_d[0] == NULL) { |
| 269 |
GError("Error: failed to allocate flast_d[0] in GreedyAlignMem!\n"); |
| 270 |
} |
| 271 |
flast_d[1] = flast_d[0] + max_d + max_d + 6; |
| 272 |
//for (int i=2;i<max_d+2;i++) { |
| 273 |
// flast_d[i]=NULL; |
| 274 |
// } |
| 275 |
//search->abmp->flast_d_affine = NULL; |
| 276 |
uplow_free = NULL; |
| 277 |
max_row_free = (int*) malloc(sizeof(int) * (max_d + 1 + d_diff)); |
| 278 |
space = new_mb_space(); |
| 279 |
} |
| 280 |
~GreedyAlignMem() { |
| 281 |
free_mb_space(space); |
| 282 |
GFREE(max_row_free); |
| 283 |
//GFREE(space); |
| 284 |
GFREE(flast_d[0]); |
| 285 |
//for (int i=0;i<max_d+2;i++) { |
| 286 |
// GFREE(flast_d[i]); |
| 287 |
// } |
| 288 |
|
| 289 |
GFREE(flast_d); |
| 290 |
} |
| 291 |
}; |
| 292 |
|
| 293 |
|
| 294 |
int get_last(int **flast_d, int d, int diag, int *row1) { |
| 295 |
if (flast_d[d-1][diag-1] > GMAX(flast_d[d-1][diag], flast_d[d-1][diag+1])) { |
| 296 |
*row1 = flast_d[d-1][diag-1]; |
| 297 |
return diag-1; |
| 298 |
} |
| 299 |
if (flast_d[d-1][diag] > flast_d[d-1][diag+1]) { |
| 300 |
*row1 = flast_d[d-1][diag]; |
| 301 |
return diag; |
| 302 |
} |
| 303 |
*row1 = flast_d[d-1][diag+1]; |
| 304 |
return diag+1; |
| 305 |
} |
| 306 |
|
| 307 |
|
| 308 |
int MegaBlastGreedyAlign(const char* s1, int len1, |
| 309 |
const char* s2, int len2, |
| 310 |
bool reverse, int xdrop_threshold, |
| 311 |
int match_cost, int mismatch_cost, |
| 312 |
int* e1, int* e2, |
| 313 |
GreedyAlignMem* abmp, SEditScript *S) |
| 314 |
// Uint1 rem) |
| 315 |
{ |
| 316 |
int col, /* column number */ |
| 317 |
d, /* current distance */ |
| 318 |
k, /* current diagonal */ |
| 319 |
flower, fupper, /* boundaries for searching diagonals */ |
| 320 |
row, /* row number */ |
| 321 |
MAX_D, /* maximum cost */ |
| 322 |
ORIGIN, |
| 323 |
return_val = 0; |
| 324 |
int** flast_d = abmp->flast_d; /* rows containing the last d */ |
| 325 |
int* max_row; /* reached for cost d=0, ... len1. */ |
| 326 |
|
| 327 |
int X_pen = xdrop_threshold; |
| 328 |
int M_half = match_cost/2; |
| 329 |
int Op_cost = mismatch_cost + M_half*2; |
| 330 |
int D_diff = (X_pen+M_half) / Op_cost + 1; |
| 331 |
int x, cur_max, b_diag = 0, best_diag = INT_MAX/2; |
| 332 |
int* max_row_free = abmp->max_row_free; |
| 333 |
char nlower = 0, nupper = 0; |
| 334 |
MBSpace* space = abmp->space; |
| 335 |
int max_len = len2; |
| 336 |
|
| 337 |
MAX_D = (int) (len1/ERROR_FRACTION + 1); |
| 338 |
ORIGIN = MAX_D + 2; |
| 339 |
GMessage("D_diff=%d, MAX_D=%d\n", D_diff, MAX_D); |
| 340 |
|
| 341 |
*e1 = *e2 = 0; |
| 342 |
//find first mismatch |
| 343 |
if (reverse) { |
| 344 |
/* |
| 345 |
if (!(rem & 4)) { |
| 346 |
for (row = 0; row < len2 && row < len1 && |
| 347 |
(s2[len2-1-row] == |
| 348 |
READDB_UNPACK_BASE_N(s1[(len1-1-row)/4], |
| 349 |
3-(len1-1-row)%4)); |
| 350 |
row++) |
| 351 |
; //empty |
| 352 |
} else { |
| 353 |
*/ |
| 354 |
for (row = 0; row < len2 && row < len1 && (s2[len2-1-row] == s1[len1-1-row]); row++) |
| 355 |
; //empty |
| 356 |
//} |
| 357 |
} else { |
| 358 |
/* |
| 359 |
if (!(rem & 4)) { |
| 360 |
for (row = 0; row < len2 && row < len1 && |
| 361 |
(s2[row] == |
| 362 |
READDB_UNPACK_BASE_N(s1[(row+rem)/4], |
| 363 |
3-(row+rem)%4)); |
| 364 |
row++) |
| 365 |
; //empty |
| 366 |
} else { */ |
| 367 |
for (row = 0; row < len2 && row < len1 && (s2[row] == s1[row]); row++) |
| 368 |
; //empty |
| 369 |
//} |
| 370 |
} |
| 371 |
*e1 = row; |
| 372 |
*e2 = row; |
| 373 |
if (row == len1) { |
| 374 |
if (S != NULL) |
| 375 |
edit_script_rep(S, row); |
| 376 |
// hit last row; stop search |
| 377 |
return 0; |
| 378 |
} |
| 379 |
if (S==NULL) |
| 380 |
space = 0; |
| 381 |
else if (!space) |
| 382 |
abmp->space = space = new_mb_space(); |
| 383 |
else |
| 384 |
refresh_mb_space(space); |
| 385 |
|
| 386 |
max_row = max_row_free + D_diff; |
| 387 |
for (k = 0; k < D_diff; k++) |
| 388 |
max_row_free[k] = 0; |
| 389 |
|
| 390 |
flast_d[0][ORIGIN] = row; |
| 391 |
max_row[0] = (row + row)*M_half; |
| 392 |
|
| 393 |
flower = ORIGIN - 1; |
| 394 |
fupper = ORIGIN + 1; |
| 395 |
|
| 396 |
d = 1; |
| 397 |
while (d <= MAX_D) { |
| 398 |
int fl0, fu0; |
| 399 |
flast_d[d - 1][flower - 1] = flast_d[d - 1][flower] = -1; |
| 400 |
flast_d[d - 1][fupper] = flast_d[d - 1][fupper + 1] = -1; |
| 401 |
x = max_row[d - D_diff] + Op_cost * d - X_pen; |
| 402 |
x = (int)ceil(x/M_half); |
| 403 |
cur_max = 0; |
| 404 |
fl0 = flower; |
| 405 |
fu0 = fupper; |
| 406 |
for (k = fl0; k <= fu0; k++) { |
| 407 |
row = GMAX(flast_d[d - 1][k + 1], flast_d[d - 1][k]) + 1; |
| 408 |
row = GMAX(row, flast_d[d - 1][k - 1]); |
| 409 |
col = row + k - ORIGIN; |
| 410 |
if (row + col >= x) |
| 411 |
fupper = k; |
| 412 |
else { |
| 413 |
if (k == flower) |
| 414 |
flower++; |
| 415 |
else |
| 416 |
flast_d[d][k] = -1; |
| 417 |
continue; |
| 418 |
} |
| 419 |
if (row > max_len || row < 0) { |
| 420 |
flower = k+1; nlower = 1; |
| 421 |
} else { |
| 422 |
/* Slide down the diagonal. Don't do this if reached |
| 423 |
the end point, which has value 0x0f */ |
| 424 |
if (reverse) { |
| 425 |
if (s2[len2-row] != 0x0f) { |
| 426 |
/*if (!(rem & 4)) |
| 427 |
while (row < len2 && col < len1 && s2[len2-1-row] == |
| 428 |
READDB_UNPACK_BASE_N(s1[(len1-1-col)/4], |
| 429 |
3-(len1-1-col)%4)) { |
| 430 |
++row; |
| 431 |
++col; |
| 432 |
} |
| 433 |
else */ |
| 434 |
while (row < len2 && col < len1 && s2[len2-1-row] == s1[len1-1-col]) { |
| 435 |
++row; |
| 436 |
++col; |
| 437 |
} |
| 438 |
} else { |
| 439 |
max_len = row; |
| 440 |
flower = k+1; nlower = 1; |
| 441 |
} |
| 442 |
} else if (s2[row-1] != 0x0f) { |
| 443 |
/*if (!(rem & 4)) { |
| 444 |
while (row < len2 && col < len1 && s2[row] == |
| 445 |
READDB_UNPACK_BASE_N(s1[(col+rem)/4], |
| 446 |
3-(col+rem)%4)) { |
| 447 |
++row; |
| 448 |
++col; |
| 449 |
} |
| 450 |
} else { */ |
| 451 |
while (row < len2 && col < len1 && s2[row] == s1[col]) { |
| 452 |
++row; |
| 453 |
++col; |
| 454 |
} |
| 455 |
// } |
| 456 |
} else { |
| 457 |
max_len = row; |
| 458 |
flower = k+1; nlower = 1; |
| 459 |
} |
| 460 |
} |
| 461 |
flast_d[d][k] = row; |
| 462 |
if (row + col > cur_max) { |
| 463 |
cur_max = row + col; |
| 464 |
b_diag = k; |
| 465 |
} |
| 466 |
if (row == len2) { |
| 467 |
flower = k+1; nlower = 1; |
| 468 |
} |
| 469 |
if (col == len1) { |
| 470 |
fupper = k-1; nupper = 1; |
| 471 |
} |
| 472 |
} //for k |
| 473 |
k = cur_max*M_half - d * Op_cost; |
| 474 |
if (max_row[d - 1] < k) { |
| 475 |
max_row[d] = k; |
| 476 |
return_val = d; |
| 477 |
best_diag = b_diag; |
| 478 |
*e2 = flast_d[d][b_diag]; |
| 479 |
*e1 = (*e2)+b_diag-ORIGIN; |
| 480 |
} else { |
| 481 |
max_row[d] = max_row[d - 1]; |
| 482 |
} |
| 483 |
if (flower > fupper) |
| 484 |
break; |
| 485 |
d++; |
| 486 |
if (!nlower) flower--; |
| 487 |
if (!nupper) fupper++; |
| 488 |
if (S==NULL) |
| 489 |
flast_d[d] = flast_d[d - 2]; |
| 490 |
else { |
| 491 |
// space array consists of ThreeVal structures which are |
| 492 |
// 3 times larger than int, so divide requested amount by 3 |
| 493 |
flast_d[d] = (int*) get_mb_space(space, (fupper-flower+7)/3); |
| 494 |
if (flast_d[d] != NULL) |
| 495 |
flast_d[d] = flast_d[d] - flower + 2; |
| 496 |
else |
| 497 |
return return_val; |
| 498 |
} |
| 499 |
} //while d<=MAX_D |
| 500 |
|
| 501 |
if (S!=NULL) { /*trace back*/ |
| 502 |
int row1, col1, diag1, diag; |
| 503 |
d = return_val; diag = best_diag; |
| 504 |
row = *e2; col = *e1; |
| 505 |
while (d > 0) { |
| 506 |
diag1 = get_last(flast_d, d, diag, &row1); |
| 507 |
col1 = row1+diag1-ORIGIN; |
| 508 |
if (diag1 == diag) { |
| 509 |
if (row-row1 > 0) edit_script_rep(S, row-row1); |
| 510 |
} else if (diag1 < diag) { |
| 511 |
if (row-row1 > 0) edit_script_rep(S, row-row1); |
| 512 |
edit_script_ins(S,1); |
| 513 |
} else { |
| 514 |
if (row-row1-1> 0) edit_script_rep(S, row-row1-1); |
| 515 |
edit_script_del(S, 1); |
| 516 |
} |
| 517 |
d--; diag = diag1; col = col1; row = row1; |
| 518 |
} //while d>0 |
| 519 |
edit_script_rep(S, flast_d[0][ORIGIN]); |
| 520 |
if (!reverse) |
| 521 |
edit_script_reverse_inplace(S); |
| 522 |
} |
| 523 |
return return_val; |
| 524 |
} |
| 525 |
|
| 526 |
|
| 527 |
#define GAPALIGN_SUB ((unsigned char)0) /*op types within the edit script*/ |
| 528 |
#define GAPALIGN_INS ((unsigned char)1) |
| 529 |
#define GAPALIGN_DEL ((unsigned char)2) |
| 530 |
#define GAPALIGN_DECLINE ((unsigned char)3) |
| 531 |
char xgapcodes[4]={'S','I', 'D', 'X'}; |
| 532 |
|
| 533 |
struct GapXEditScript { |
| 534 |
unsigned char op_type; // GAPALIGN_SUB, GAPALIGN_INS, or GAPALIGN_DEL |
| 535 |
int num; // Number of operations |
| 536 |
GapXEditScript* next; |
| 537 |
GapXEditScript() { |
| 538 |
op_type=0; |
| 539 |
num=0; |
| 540 |
next=NULL; |
| 541 |
} |
| 542 |
}; |
| 543 |
|
| 544 |
class CSeqGap { // |
| 545 |
public: |
| 546 |
int offset; |
| 547 |
int len; |
| 548 |
CSeqGap(int gofs=0,int glen=1) { |
| 549 |
offset=gofs; |
| 550 |
len=glen; |
| 551 |
} |
| 552 |
}; |
| 553 |
|
| 554 |
class CAlnGapInfo { |
| 555 |
int a_ofs; //alignment start on seq a (0 based) |
| 556 |
int b_ofs; //alignment start on seq b (0 based) |
| 557 |
int a_len; //length of alignment on seq a |
| 558 |
int b_len; //length of alignment on seq b |
| 559 |
public: |
| 560 |
GVec<CSeqGap> a_gaps; |
| 561 |
GVec<CSeqGap> b_gaps; |
| 562 |
CAlnGapInfo(SEditScript* ed_script, int astart=0, int bstart=0):a_gaps(),b_gaps() { |
| 563 |
a_ofs=astart; |
| 564 |
b_ofs=bstart; |
| 565 |
a_len=0; |
| 566 |
b_len=0; |
| 567 |
for (int i=0; i<ed_script->num; i++) { |
| 568 |
int num=((ed_script->op[i]) >> 2); |
| 569 |
char op_type = 3 - ( ed_script->op[i] & EDIT_OP_MASK ); |
| 570 |
if (op_type == 3 || op_type < 0 ) |
| 571 |
GError("Error: encountered op_type %d in ed_script?!\n", (int)op_type); |
| 572 |
CSeqGap gap; |
| 573 |
switch (op_type) { |
| 574 |
case GAPALIGN_SUB: a_len+=num; |
| 575 |
b_len+=num; |
| 576 |
break; |
| 577 |
case GAPALIGN_INS: a_len+=num; |
| 578 |
gap.offset=b_ofs+b_len; |
| 579 |
gap.len=num; |
| 580 |
b_gaps.Add(gap); |
| 581 |
break; |
| 582 |
case GAPALIGN_DEL: b_len+=num; |
| 583 |
gap.offset=a_ofs+a_len; |
| 584 |
gap.len=num; |
| 585 |
a_gaps.Add(gap); |
| 586 |
break; |
| 587 |
} |
| 588 |
} |
| 589 |
} |
| 590 |
void printSeqA(const char* s) { |
| 591 |
int g=0; |
| 592 |
int aend=a_ofs+a_len; |
| 593 |
for (int i=a_ofs;i<aend;i++) { |
| 594 |
if (g<a_gaps.Count() && a_gaps[g].offset==i) { |
| 595 |
for (int j=0;j<a_gaps[g].len;j++) fprintf(stderr, "-"); |
| 596 |
g++; |
| 597 |
} |
| 598 |
fprintf(stderr, "%c", s[i]); |
| 599 |
} |
| 600 |
fprintf(stderr, "\n"); |
| 601 |
} |
| 602 |
void printSeqB(const char* s) { |
| 603 |
int g=0; |
| 604 |
int bend=b_ofs+b_len; |
| 605 |
for (int i=b_ofs;i<bend;i++) { |
| 606 |
if (g<b_gaps.Count() && b_gaps[g].offset==i) { |
| 607 |
for (int j=0;j<b_gaps[g].len;j++) fprintf(stderr, "-"); |
| 608 |
g++; |
| 609 |
} |
| 610 |
fprintf(stderr, "%c", s[i]); |
| 611 |
} |
| 612 |
fprintf(stderr, "\n"); |
| 613 |
} |
| 614 |
}; |
| 615 |
|
| 616 |
GapXEditScript* EditScript2GapX(SEditScript* ed_script) { |
| 617 |
GapXEditScript* esp_array=NULL; |
| 618 |
uint i; |
| 619 |
if (ed_script==NULL || ed_script->num == 0) |
| 620 |
return NULL; |
| 621 |
//GMALLOC(esp_array, ed_script->num * sizeof(GapXEditScript)); |
| 622 |
esp_array = new GapXEditScript[ed_script->num]; |
| 623 |
for (i=0; i<ed_script->num; i++) { |
| 624 |
//GCALLOC(esp, sizeof(GapXEditScript)); |
| 625 |
//esp->num = EDIT_VAL(ed_script->op[i]); |
| 626 |
//esp->num = ((ed_script->op[i]) >> 2); |
| 627 |
esp_array[i].num=((ed_script->op[i]) >> 2); |
| 628 |
//esp->op_type = 3 - EDIT_OPC(ed_script->op[i]); |
| 629 |
//esp->op_type = 3 - ( ed_script->op[i] & EDIT_OP_MASK ); |
| 630 |
esp_array[i].op_type = 3 - ( ed_script->op[i] & EDIT_OP_MASK ); |
| 631 |
if (esp_array[i].op_type == 3) |
| 632 |
//fprintf(stderr, "op_type = 3\n"); |
| 633 |
GError("Error: EditScript2GapX encountered op_type 3 ?!\n"); |
| 634 |
if (i>0) |
| 635 |
esp_array[i-1].next=&esp_array[i]; |
| 636 |
} |
| 637 |
return esp_array; |
| 638 |
} |
| 639 |
|
| 640 |
|
| 641 |
|
| 642 |
struct GappedHSPInfo { |
| 643 |
const char *qseq; |
| 644 |
int ql,qr; |
| 645 |
const char *sseq; |
| 646 |
int sl,sr; |
| 647 |
int score; |
| 648 |
double pid; |
| 649 |
GapXEditScript* editscript; |
| 650 |
CAlnGapInfo* gapinfo; |
| 651 |
GappedHSPInfo(const char* q, int q_l, int q_r, const char* s, int s_l, int s_r, |
| 652 |
int sc=0, double percid=0) { |
| 653 |
qseq=q; |
| 654 |
sseq=s; |
| 655 |
ql=q_l; |
| 656 |
qr=q_r; |
| 657 |
sl=s_l; |
| 658 |
sr=s_r; |
| 659 |
score=sc; |
| 660 |
pid=percid; |
| 661 |
editscript=NULL; |
| 662 |
gapinfo=NULL; |
| 663 |
} |
| 664 |
~GappedHSPInfo() { |
| 665 |
delete[] editscript; |
| 666 |
delete gapinfo; |
| 667 |
} |
| 668 |
}; |
| 669 |
|
| 670 |
GappedHSPInfo* GreedyAlign(const char* q_seq, int q_off, const char* s_seq, int s_off, |
| 671 |
int reward, int penalty, int xdrop) { |
| 672 |
|
| 673 |
SEditScript* ed_script_fwd = edit_script_new(); |
| 674 |
SEditScript* ed_script_rev = edit_script_new(); |
| 675 |
int q_ext_l=0, q_ext_r=0, s_ext_l=0, s_ext_r=0; |
| 676 |
int score=0; |
| 677 |
int slen=strlen(s_seq); //subj |
| 678 |
int qlen=strlen(q_seq); //query |
| 679 |
const char* q=q_seq+q_off; |
| 680 |
int q_avail=qlen-q_off; |
| 681 |
const char* s=s_seq+s_off; |
| 682 |
int s_avail=slen-s_off; |
| 683 |
int MIN_GREEDY_SCORE=5; //minimum score for an alignment to be reported |
| 684 |
GreedyAlignMem* abmp=new GreedyAlignMem(slen, reward, -penalty, xdrop); |
| 685 |
// extend to the right |
| 686 |
score = MegaBlastGreedyAlign(s, s_avail, q, q_avail, false, xdrop, |
| 687 |
reward, -penalty, &s_ext_r, &q_ext_r, abmp, ed_script_fwd); |
| 688 |
GMessage("fwd score=%d (up to a_r=%d, b_r=%d)\n", score, q_ext_r, s_ext_r); |
| 689 |
/* extend to the left */ |
| 690 |
score += MegaBlastGreedyAlign(s_seq, s_off, q_seq, q_off, true, xdrop, |
| 691 |
reward, -penalty, &s_ext_l, &q_ext_l, abmp, ed_script_rev); |
| 692 |
GMessage("rvs score=%d (back to a_l=%d, b_l=%d)\n", score, q_ext_l, s_ext_l); |
| 693 |
delete abmp; |
| 694 |
GappedHSPInfo* ghsp=NULL; |
| 695 |
// In basic case the greedy algorithm returns number of |
| 696 |
// differences, hence we need to convert it to score |
| 697 |
int retscore = (q_ext_r + s_ext_r + q_ext_l + s_ext_l)*reward/2 - score*(reward-penalty); |
| 698 |
GMessage("Actual score: %d\n",retscore); |
| 699 |
edit_script_append(ed_script_rev, ed_script_fwd); //combine the two extensions |
| 700 |
if (retscore>=MIN_GREEDY_SCORE) { |
| 701 |
ghsp=new GappedHSPInfo(q_seq, q_ext_l,q_ext_r, s_seq, s_ext_l, s_ext_r); |
| 702 |
int hsp_length = GMIN(q_ext_l+q_ext_r, s_ext_l+s_ext_r); |
| 703 |
ghsp->score=retscore; |
| 704 |
ghsp->pid = 100 * (1 - ((double) score) / hsp_length); |
| 705 |
//ghsp->editscript = EditScript2GapX(ed_script_rev); |
| 706 |
|
| 707 |
ghsp->gapinfo = new CAlnGapInfo(ed_script_rev, ghsp->ql, ghsp->sl); |
| 708 |
edit_script_free(ed_script_rev); |
| 709 |
edit_script_free(ed_script_fwd); |
| 710 |
} |
| 711 |
return ghsp; |
| 712 |
} |
| 713 |
|
| 714 |
#define FRCLOSE(fh) if (fh!=NULL && fh!=stdin) fclose(fh) |
| 715 |
#define FWCLOSE(fh) if (fh!=NULL && fh!=stdout) fclose(fh) |
| 716 |
|
| 717 |
char* seq_cleanup(const char* s) { |
| 718 |
char* r=NULL; |
| 719 |
int slen=strlen(s); |
| 720 |
GMALLOC(r, slen+1); |
| 721 |
int newlen=0; |
| 722 |
for (int i=0;i<slen;i++) { |
| 723 |
if (s[i]<'A' || s[i]>'z' || (s[i]>'Z' && s[i]<'a')) continue; |
| 724 |
r[newlen]=s[i]; |
| 725 |
newlen++; |
| 726 |
} |
| 727 |
r[newlen]=0; |
| 728 |
return r; |
| 729 |
} |
| 730 |
|
| 731 |
void loadSeqs(const char* fname, char*& s1, char*& s2) { |
| 732 |
GLineReader lr(fname); |
| 733 |
char* l=NULL; |
| 734 |
s1=NULL; |
| 735 |
s2=NULL; |
| 736 |
while ((l=lr.nextLine())!=NULL) { |
| 737 |
if (lr.length()<=3 || l[0]=='#') continue; |
| 738 |
if (s1==NULL) { |
| 739 |
s1=seq_cleanup(l); |
| 740 |
} |
| 741 |
else if (s2==NULL) s2=seq_cleanup(l); |
| 742 |
else break; |
| 743 |
} |
| 744 |
} |
| 745 |
|
| 746 |
//================= MAIN ===================== |
| 747 |
|
| 748 |
int main(int argc, char * const argv[]) { |
| 749 |
GArgs args(argc, argv, "a:b:i:"); |
| 750 |
int e; |
| 751 |
if ((e=args.isError())>0) |
| 752 |
GError("%s\nInvalid argument: %s\n", USAGE, argv[e]); |
| 753 |
if (args.getOpt('h')!=NULL) GError("%s\n", USAGE); |
| 754 |
char* seqa=NULL; |
| 755 |
char* seqb=NULL; |
| 756 |
GStr s=args.getOpt('i'); |
| 757 |
if (!s.is_empty()) loadSeqs(s.chars(), seqa, seqb); |
| 758 |
else { |
| 759 |
s=args.getOpt('a'); |
| 760 |
if (!s.is_empty()) seqa=seq_cleanup(s.chars()); |
| 761 |
s=args.getOpt('b'); |
| 762 |
if (!s.is_empty()) seqb=seq_cleanup(s.chars()); |
| 763 |
} |
| 764 |
if (seqa==NULL || seqb==NULL) GError("Error: both sequences are required!\n"); |
| 765 |
GMessage("seqa: %s\n",seqa); |
| 766 |
GMessage("seqb: %s\n",seqb); |
| 767 |
//offsets must be in the middle of a good (best) HSP (ungapped match) |
| 768 |
GappedHSPInfo* ghsp=GreedyAlign(seqa, 0, seqb, 0, 2, -3, 22); |
| 769 |
if (ghsp!=NULL) { |
| 770 |
GMessage("a(%d..%d) align to b(%d..%d), score=%d, pid=%4.2f\n", ghsp->ql, ghsp->qr, |
| 771 |
ghsp->sl, ghsp->sr, ghsp->score, ghsp->pid); |
| 772 |
if (ghsp->editscript!=NULL) { |
| 773 |
GMessage("Edit script: "); |
| 774 |
GapXEditScript* ges=ghsp->editscript; |
| 775 |
do { |
| 776 |
GMessage("%d%c ",ges->num, xgapcodes[ges->op_type]); |
| 777 |
} while ((ges=ges->next)!=NULL); |
| 778 |
GMessage("\n"); |
| 779 |
} |
| 780 |
if (ghsp->gapinfo!=NULL) { |
| 781 |
GMessage("Alignment:\n"); |
| 782 |
ghsp->gapinfo->printSeqA(seqa); |
| 783 |
ghsp->gapinfo->printSeqB(seqb); |
| 784 |
} |
| 785 |
delete ghsp; |
| 786 |
} |
| 787 |
//---- done here |
| 788 |
GFREE(seqa); |
| 789 |
GFREE(seqb); |
| 790 |
} |
