ecoprimer.c 14.6 KB
Newer Older
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472
/*
 * ecoprimer.c
 *
 *  Created on: 7 nov. 2008
 *      Author: coissac
 */

#include "libecoprimer/ecoprimer.h"
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <getopt.h>
#include <time.h>
#include <sys/time.h>

#define VERSION "0.1"
  /* TR: by default, statistics are made on species level*/
#define DEFULTTAXONRANK "species"

/* ----------------------------------------------- */
/* printout help                                   */
/* ----------------------------------------------- */
#define PP fprintf(stdout,

static void PrintHelp()
{
        PP      "------------------------------------------\n");
        PP      " ecoPrimer Version %s\n", VERSION);
        PP      "------------------------------------------\n");
}

static void ExitUsage(int stat)
{
        PP      "usage: ecoprimer [-d database] [-l value] [-L value] [-e value] [-r taxid] [-i taxid] [-R rank] [-t taxon level]\n");
        PP      "type \"ecoprimer -h\" for help\n");

        if (stat)
            exit(stat);
}

#undef  PP

void initoptions(poptions_t options)
{
	options->lmin=0;                   //< Amplifia minimal length
	options->lmax=0;                   //< Amplifia maximal length
	options->error_max=3;              //**< maximum error count in fuzzy search
	options->primer_length=18;          //**< minimal length of the primers
	options->restricted_taxid=NULL;      //**< limit amplification below these taxid
	options->ignored_taxid=NULL;         //**< no amplification below these taxid
	options->prefix=NULL;
	options->circular=0;
	options->doublestrand=1;
	options->strict_quorum=0.7;
	options->strict_exclude_quorum=0.1;
	options->sensitivity_quorum=0.9;
	options->false_positive_quorum=0.1;
	options->strict_three_prime=2;
	options->r=0;
	options->g=0;
	options->no_multi_match=FALSE;
	strcpy(options->taxonrank, DEFULTTAXONRANK);			/*taxon level for results, species by default*/
}

void printcurrenttime ()
{
    time_t     now;
    struct tm  *ts;
    char       buf[80];

    /* Get the current time */
    now = time(NULL);

    /* Format and print the time, "ddd yyyy-mm-dd hh:mm:ss zzz" */
    ts = localtime(&now);
    strftime(buf, sizeof(buf), "%a %Y-%m-%d %H:%M:%S %Z", ts);
    fprintf(stderr,"#%d#, %s\n",now, buf);
 }

void printcurrenttimeinmilli()
{
     struct timeval tv;
     struct timezone tz;
     struct tm *tm;
     gettimeofday(&tv, &tz);
     tm=localtime(&tv.tv_sec);
     fprintf(stderr, " %d:%02d:%02d %d %d \n", tm->tm_hour, tm->tm_min,
              tm->tm_sec, tv.tv_usec, tv.tv_usec/1000);
}

/*TR: Added*/
void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize)
{
	uint32_t i;
	uint32_t  wordsize = options->primer_length;
	uint32_t	 quorumseqs;
	double sens;
	double speci;
	float  avg;
	
	quorumseqs = seqdbsize * 70 / 100;
	
	printf("primer_1\tseq_1\tPrimer_2\tseq_2\tamplifia_count\t%s_snes\t%s_spe\tmin_l\tmax_l\tavr_l\n", options->taxonrank, options->taxonrank);

	for (i=0; i < pairs.paircount; i++)
	{
		if (quorumseqs > pairs.pairs[i].inexample) continue;
		sens = (pairs.pairs[i].taxsetindex*1.0)/rankdbstats*100;
		speci = (pairs.pairs[i].oktaxoncount*1.0)/pairs.pairs[i].taxsetindex*100;
		avg = (pairs.pairs[i].mind+pairs.pairs[i].maxd)*1.0/2;

		printf("P1\t%s", ecoUnhashWord(pairs.pairs[i].w1, wordsize));
		printf("\tP2\t%s", ecoUnhashWord(pairs.pairs[i].w2, wordsize));
		printf("\t%d", pairs.pairs[i].inexample);
		printf("\t%3.2f", sens);
		printf("\t%3.2f", speci);
		printf("\t%d", pairs.pairs[i].mind);
		printf("\t%d", pairs.pairs[i].maxd);
		printf("\t%3.2f\n", avg);
	}
}

/*updateseqparams: This function counts the insample and outsample sequences
 *  and with each sequences adds a tag of the taxon to which the sequence beongs*/
void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy, 
		poptions_t options, int32_t *insamples, int32_t *outsamples)
{
	uint32_t i;
	int32_t taxid;
	ecotx_t  *tmptaxon;

    for (i=0;i<seqdbsize;i++)
    {    	
    	seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
    	if (seqdb[i]->isexample)
    		(*insamples)++;
    	else
    		(*outsamples)++;

    	taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid;
		tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);		
		if (tmptaxon)
			tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx);
		if (tmptaxon)
			seqdb[i]->ranktaxonid = tmptaxon->taxid;
    }
}

void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
{
	int32_t i;

    /*set taxon rank for which result is to be given*/
    for (i = 0; i < taxonomy->ranks->count; i++)
    {
    	if (strcmp(taxonomy->ranks->label[i], options->taxonrank) == 0) 
    	{
    		options->taxonrankidx = i;
    		break;
    	}
    }

    if (i == taxonomy->ranks->count)
    {
    	fprintf(stderr,"\nUnknown taxon level: '%s'\n", options->taxonrank);
    	exit(0);
    }
}
/* to get db stats, totals of species, genus etc....*/
int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy, 
		poptions_t options)
{
	uint32_t i;
	uint32_t j;
	uint32_t nameslots = 500;
	uint32_t namesindex = 0;
	int32_t *ranktaxonids = ECOMALLOC(nameslots * sizeof(int32_t), "Error in taxon rank allocation");
	int32_t taxid;
	
	ecotx_t  *tmptaxon;

    for (i=0;i<seqdbsize;i++)
	{
    	taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid;
		tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);
		if (tmptaxon)
			tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx);
		if (tmptaxon)
		{
			for (j = 0; j < namesindex; j++)
			{
				if (tmptaxon->taxid == ranktaxonids[j]) break;
			}
			if (j < namesindex) continue; /* name is already in list, so no need to add it*/
			
			if (namesindex == nameslots)
			{
				nameslots += 500;
				ranktaxonids = ECOREALLOC(ranktaxonids, nameslots * sizeof(int32_t), "Cannot allocate pair rank taxon table");
			}
			ranktaxonids[namesindex] = tmptaxon->taxid;
			namesindex++;
		}
	}
    ECOFREE(ranktaxonids, "free rank taxon table");
    
    return namesindex;
}

void setoktaxforspecificity (ppairscount_t pairs)
{
	uint32_t i;
	uint32_t j;
	uint32_t k;
	uint32_t l;
	int taxcount;
	int32_t taxid;
	
	for (i = 0; i < pairs->paircount; i++)
	{
		for (j = 0; j < pairs->pairs[i].taxsetindex; j++)
		{
			for (k = 0; k < pairs->pairs[i].taxset[j].amplifiaindex; k++)
			{
				taxid = 0;
				taxcount = 0;
				for (l = 0; l < pairs->pairs[i].ampsetindex; l++)
				{
					/*compare only char pointers because for equal strings we have same pointer in both sets*/
					if (pairs->pairs[i].taxset[j].amplifia[k] == pairs->pairs[i].ampset[l].amplifia)
					{
						if (pairs->pairs[i].ampset[l].seqidindex > 1)
						{
							taxcount += pairs->pairs[i].ampset[l].seqidindex;
							break;
						}
						
						if (taxid != pairs->pairs[i].ampset[l].taxonids[0])
						{
							if (!taxid) taxid = pairs->pairs[i].ampset[l].taxonids[0];
							taxcount++;	
						}
						
						if (taxcount > 1) break;
					}
				}
				if (taxcount == 1) pairs->pairs[i].oktaxoncount++;
			}
		}
	}
}

int main(int argc, char **argv)
{
	pecodnadb_t   seqdb; /* of type ecoseq_t */
	uint32_t        seqdbsize=0;
	ecotaxonomy_t *taxonomy;

	options_t     options;
	int           carg;
	int32_t       errflag=0;

	int32_t       insamples=0;
	int32_t       outsamples=0;
	uint32_t        i;
	
	pwordcount_t  words;
	pprimercount_t     primers;
	pairscount_t		pairs;
	
	int32_t		  rankdbstats = 0;

	//printcurrenttime();
	//return 0;

	initoptions(&options);

    while ((carg = getopt(argc, argv, "hcUDSd:l:L:e:i:r:q:3:s:x:t:")) != -1) {

     switch (carg) {
                                /* -------------------- */
        case 'd':               /* database name        */
                                /* -------------------- */
        	options.prefix = ECOMALLOC(strlen(optarg)+1,
                              "Error on prefix allocation");
           strcpy(options.prefix,optarg);
           break;

                                /* -------------------- */
        case 'h':               /* help                 */
                                /* -------------------- */
           PrintHelp();
           exit(0);
           break;

                                /* ------------------------- */
        case 'l':               /* min amplification lenght  */
                                /* ------------------------- */
           sscanf(optarg,"%d",&(options.lmin));
           break;

                                /* -------------------------- */
        case 'L':               /* max amplification lenght   */
                                /* -------------------------- */
          sscanf(optarg,"%d",&(options.lmax));
          break;

                                /* -------------------- */
        case 'e':               /* error max            */
                                /* -------------------- */
          sscanf(optarg,"%d",&(options.error_max));
          break;


								/* ------------------------ */
		case '3':               /* three prime strict match */
                                /* ------------------------ */
			sscanf(optarg,"%d",&(options.strict_three_prime));
			break;

                                /* -------------------- */
        case 'q':               /* strict matching quorum           */
                                /* -------------------- */
          sscanf(optarg,"%f",&(options.strict_quorum));
          break;

								/* -------------------- */
        case 's':               /* strict matching quorum      */
								/* -------------------- */
        	sscanf(optarg,"%f",&(options.sensitivity_quorum));
        	break;

        						/* -------------------- */
        case 't':               /* required taxon level for results           */
        						/* -------------------- */
        	strncpy(options.taxonrank, optarg, 19);
        	options.taxonrank[19] = 0;
            break;
        	
        						/* -------------------- */
        case 'x':               /* strict matching quorum           */
								/* -------------------- */
        	sscanf(optarg,"%f",&(options.false_positive_quorum));
        	break;

							    /* ---------------------------- */
		case 'D':               /* set in double strand mode    */
							    /* ---------------------------- */
			options.doublestrand=1;
			break;

								/* ---------------------------- */
		case 'S':               /* set in single strand mode    */
								/* ---------------------------- */
			options.doublestrand=0;
			break;

			                    /* ---------------------------- */
        case 'U':               /* set in single strand mode    */
			                    /* ---------------------------- */
            options.no_multi_match=TRUE;
            break;

         						/* ------------------------------------------ */
        case 'r':               /* stores the restricting search taxonomic id */
        						/* ------------------------------------------ */
          options.restricted_taxid = ECOREALLOC(options.restricted_taxid,sizeof(int32_t)*(options.r+1),
          									"Error on restricted_taxid reallocation");
          sscanf(optarg,"%d",&(options.restricted_taxid[options.r]));
          options.r++;
          break;

         						/* --------------------------------- */
        case 'i':               /* stores the taxonomic id to ignore */
        						/* --------------------------------- */
          options.ignored_taxid = ECOREALLOC(options.ignored_taxid,sizeof(int32_t)*(options.g+1),
          									"Error on excluded_taxid reallocation");
          sscanf(optarg,"%d",&(options.ignored_taxid[options.g]));
          options.g++;
          break;

                                /* -------------------- */
        case 'c':               /* sequences are circular */
        						/* --------------------------------- */
		  options.circular = 1;
          break;

        case '?':               /* bad option           */
                                /* -------------------- */
            errflag++;
   		}

	}

    fprintf(stderr,"Reading taxonomy database ...");
    taxonomy = read_taxonomy(options.prefix,0);
    fprintf(stderr,"Ok\n");
    
    setresulttaxonrank(taxonomy, &options); /*TR: set rank level for statistics*/
    
    fprintf(stderr,"Reading sequence database ...\n");

    seqdb = readdnadb(options.prefix,&seqdbsize);

    fprintf(stderr,"Ok\n");
    fprintf(stderr,"Sequence read : %d\n",(int32_t)seqdbsize);
    
    updateseqparams(seqdb, seqdbsize, taxonomy, &options, &insamples , &outsamples);

    rankdbstats = getrankdbstats(seqdb, seqdbsize, taxonomy, &options);

    fprintf(stderr,"Database is constituted of %5d examples\n",insamples);
    fprintf(stderr,"                       and %5d counterexamples\n",outsamples);
    fprintf(stderr,"Total distinct %s count %d\n",options.taxonrank, rankdbstats);

    fprintf(stderr,"\nIndexing words in sequences\n");

    printcurrenttimeinmilli();
    words = lookforStrictPrimer(seqdb,seqdbsize,insamples,&options);
    printcurrenttimeinmilli();
    
    fprintf(stderr,"\n  Strict primer count : %d\n",words->size);

    if (options.no_multi_match)
    {
    	(void)filterMultiStrictPrimer(words);
    	fprintf(stderr,"\n  Strict primer with single match count : %d\n",words->size);
    }


    fprintf(stderr,"\n\n  Primer sample : \n");
    for (i=0; i<MINI(10,words->size); i++)
    	fprintf(stderr,"  + Primer : %s   sequence count : %d\n",ecoUnhashWord(words->words[i],options.primer_length),words->strictcount[i]);


    fprintf(stderr,"\nEncoding sequences for fuzzy pattern matching...\n");
    for (i=0;i<seqdbsize;i++)
    {
    	encodeSequence(seqdb[i]);
    	fprintf(stderr,"  Encoded sequences %5d/%5d          \r",(int32_t)i+1,(int32_t)seqdbsize);
    }

    ECOFREE(words->strictcount,"Free strict primer count table");

    primers = lookforAproxPrimer(seqdb,seqdbsize,insamples,words,&options);

    ECOFREE(words->words,"Free strict primer table");
    ECOFREE(words,"Free strict primer structure");
    fprintf(stderr,"\n\n  Approximate repeats :%d \n", primers->size);

    fprintf(stderr,"\n\n  Primer sample : \n");
    for (i=0; i<MINI(10,primers->size); i++)
    	fprintf(stderr,"  + Primer : %s   example sequence count : %5d counterexample sequence count : %5d  status : %s\n",ecoUnhashWord(primers->primers[i].word,options.primer_length),
                       primers->primers[i].inexample,
                       primers->primers[i].outexample,
                       primers->primers[i].good ? "good":"bad");

    fprintf(stderr,"\n");

    /*TR: Added*/
    pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
    setoktaxforspecificity (&pairs);
    
    printpairs (pairs, &options, rankdbstats, seqdbsize);
    
    
    
    ECOFREE(pairs.pairs,"Free pairs table");

    return 0;
}