First run of patch
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@203 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
160
src/ecoprimer.c
160
src/ecoprimer.c
@ -16,7 +16,10 @@
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#define VERSION "0.1"
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/* TR: by default, statistics are made on species level*/
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#define DEFULTTAXONRANK "species"
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#define DEFAULTTAXONRANK "species"
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static int cmpprintedpairs(const void* p1,const void* p2);
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/* ----------------------------------------------- */
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/* printout help */
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@ -40,7 +43,7 @@ static void PrintHelp()
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PP " .tdx : contains information concerning the taxonomy\n");
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PP " .rdx : contains the taxonomy rank\n\n");
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PP " ecoPrimer needs all the file type. As a result, you have to write the\n");
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PP " database radical without any extension. For example /ecoPrimerDB/fstvert\n\n");
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PP " database radical without any extension. For example /ecoPrimerDB/fstvert\n\n");
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PP "-e : [E]rror : max error allowed by oligonucleotide (0 by default)\n\n");
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PP "-h : [H]elp - print <this> help\n\n");
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PP "-i : [I]gnore the given taxonomy id.\n\n");
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@ -69,13 +72,14 @@ static void PrintHelp()
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PP "column 8 : in taxa count\n");
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PP "column 9 : out taxa count\n");
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PP "column 10 : coverage\n");
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PP "column 11 : specificity\n");
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PP "column 12 : minimum amplified length\n");
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PP "column 13 : maximum amplified length\n");
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PP "column 14 : average amplified length\n");
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PP "column 11 : unambiguously identified taxa\n");
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PP "column 12 : specificity\n");
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PP "column 13 : minimum amplified length\n");
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PP "column 14 : maximum amplified length\n");
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PP "column 15 : average amplified length\n");
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PP "------------------------------------------\n");
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PP " http://www.grenoble.prabi.fr/trac/ecoPrimer/\n");
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PP "------------------------------------------\n\n");
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PP "------------------------------------------\n\n");
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PP "\n");
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}
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@ -110,7 +114,7 @@ void initoptions(poptions_t options)
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options->r=0;
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options->g=0;
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options->no_multi_match=FALSE;
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strcpy(options->taxonrank, DEFULTTAXONRANK); /*taxon level for results, species by default*/
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strcpy(options->taxonrank, DEFAULTTAXONRANK); /*taxon level for results, species by default*/
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}
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void printcurrenttime ()
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@ -143,8 +147,7 @@ void printcurrenttimeinmilli()
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void printapair(int32_t index,ppair_t pair, poptions_t options)
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{
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uint32_t wellidentifiedtaxa;
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printf("%6d\t",index);
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if (pair->asdirect1)
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printf("%s\t",ecoUnhashWord(pair->p1->word,options->primer_length));
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@ -167,17 +170,11 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
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printf("\t%d", pair->intaxa);
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printf("\t%d", pair->outtaxa);
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printf("\t%4.3f", (float)pair->intaxa/options->intaxa);
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wellidentifiedtaxa = (pair->intaxa + pair->outtaxa) - pair->notwellidentifiedtaxa;
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//printf("\t%d", pair->notwellidentifiedtaxa);
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//printf("\t%d", (pair->intaxa + pair->outtaxa));
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printf("\t%4.3f", (float)pair->bc);
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printf("\t%d", pair->intaxa - pair->notwellidentifiedtaxa);
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printf("\t%4.3f", (float)wellidentifiedtaxa/(options->intaxa + options->outtaxa));
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printf("\t%4.3f", pair->bs);
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printf("\t%d", pair->mind);
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@ -186,6 +183,25 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
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}
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static int cmpprintedpairs(const void* p1,const void* p2)
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{
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float s1,s2;
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ppair_t pair1,pair2;
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pair1=*((ppair_t*)p1);
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pair2=*((ppair_t*)p2);
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s1 = pair1->yule * pair1->bs;
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s2 = pair2->yule * pair2->bs;
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// fprintf(stderr,"s1 : %4.3f %4.3f %4.3f\n",pair1->yule , pair1->bs,s1);
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// fprintf(stderr,"s2 : %4.3f %4.3f %4.3f\n\n",pair2->yule , pair2->bs,s2);
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if (s1 > s2) return -1;
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if (s1 < s2) return 1;
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return 0;
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}
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uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t options)
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{
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uint32_t i,j;
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@ -201,9 +217,10 @@ uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t opti
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qfp = (float)sortedpairs[i]->outexample/options->outsamples;
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else qfp=0.0;
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sortedpairs[i]->quorumin = q;
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sortedpairs[i]->quorumout = qfp;
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sortedpairs[i]->yule = q -qfp;
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sortedpairs[i]->yule = q - qfp;
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sortedpairs[j]=sortedpairs[i];
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@ -215,23 +232,30 @@ uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t opti
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{
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(void)taxonomycoverage(sortedpairs[j],options);
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taxonomyspecificity(sortedpairs[j]);
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// fprintf(stderr,"%4.3f %4.3f %4.3f\n",sortedpairs[j]->yule , sortedpairs[j]->bs,sortedpairs[j]->bc);
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j++;
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}
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}
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qsort(sortedpairs,j,sizeof(ppair_t),cmpprintedpairs);
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return j;
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}
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void printpairs (ppairtree_t pairs, poptions_t options)
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{
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ppair_t* sortedpairs;
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ppair_t* index;
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ppairlist_t pl;
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size_t i,j;
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int32_t count;
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size_t count;
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//printf("Index\tPrimer1\tPrimer2\tGB\tInexampleCount\tOutexampleCount\tYule\tIntaxaCount\tOuttaxaCount\tCoverage\tSpecificity\tMinAmplifiedLength\tMaxAmplifiedLength\tAvgAmplifiedLength\n");
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//printf("Index\tPrimer1\tPrimer2\tGB\tInexampleCount\tOutexampleCount\tYule\tIntaxaCount\tOuttaxaCount\tCoverage\tSpecificity\tMinAmplifiedLength\tMaxAmplifiedLength\tAvgAmplifiedLength\n");
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fprintf(stderr,"Total pair count : %d\n",pairs->count);
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sortedpairs = ECOMALLOC(pairs->count*sizeof(ppair_t),"Cannot Allocate ordered pairs");
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@ -256,40 +280,6 @@ void printpairs (ppairtree_t pairs, poptions_t options)
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}
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#ifdef MASKEDCODE
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void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize)
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{
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uint32_t i;
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uint32_t wordsize = options->primer_length;
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uint32_t quorumseqs;
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double sens;
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double speci;
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float avg;
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quorumseqs = seqdbsize * 70 / 100;
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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);
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for (i=0; i < pairs.paircount; i++)
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{
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if (quorumseqs > pairs.pairs[i].inexample) continue;
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sens = (pairs.pairs[i].taxsetindex*1.0)/rankdbstats*100;
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speci = (pairs.pairs[i].oktaxoncount*1.0)/pairs.pairs[i].taxsetindex*100;
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avg = (pairs.pairs[i].mind+pairs.pairs[i].maxd)*1.0/2;
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printf("P1\t%s", ecoUnhashWord(pairs.pairs[i].w1, wordsize));
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printf("\tP2\t%s", ecoUnhashWord(pairs.pairs[i].w2, wordsize));
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printf("\t%d", pairs.pairs[i].inexample);
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printf("\t%3.2f", sens);
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printf("\t%3.2f", speci);
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printf("\t%d", pairs.pairs[i].mind);
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printf("\t%d", pairs.pairs[i].maxd);
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printf("\t%3.2f\n", avg);
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}
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}
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#endif /* MASKEDCODE */
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/*updateseqparams: This function counts the insample and outsample sequences
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* and with each sequences adds a tag of the taxon to which the sequence beongs*/
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@ -340,52 +330,6 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
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}
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/* to get db stats, totals of species, genus etc....*/
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#ifdef MASKEDCODE
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void setoktaxforspecificity (ppairtree_t pairs)
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{
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uint32_t i;
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uint32_t j;
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uint32_t k;
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uint32_t l;
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int taxcount;
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int32_t taxid;
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for (i = 0; i < pairs->paircount; i++)
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{
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for (j = 0; j < pairs->pairs[i].taxsetindex; j++)
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{
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for (k = 0; k < pairs->pairs[i].taxset[j].amplifiaindex; k++)
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{
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taxid = 0;
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taxcount = 0;
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for (l = 0; l < pairs->pairs[i].ampsetindex; l++)
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{
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/*compare only char pointers because for equal strings we have same pointer in both sets*/
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if (pairs->pairs[i].taxset[j].amplifia[k] == pairs->pairs[i].ampset[l].amplifia)
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{
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if (pairs->pairs[i].ampset[l].seqidindex > 1)
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{
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taxcount += pairs->pairs[i].ampset[l].seqidindex;
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break;
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}
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if (taxid != pairs->pairs[i].ampset[l].taxonids[0])
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{
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if (!taxid) taxid = pairs->pairs[i].ampset[l].taxonids[0];
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taxcount++;
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}
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if (taxcount > 1) break;
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}
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}
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if (taxcount == 1) pairs->pairs[i].oktaxoncount++;
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}
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}
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}
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}
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#endif
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int main(int argc, char **argv)
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{
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@ -412,7 +356,7 @@ int main(int argc, char **argv)
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initoptions(&options);
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while ((carg = getopt(argc, argv, "hcUDSd:l:L:e:i:r:q:3:s:x:t:")) != -1) {
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while ((carg = getopt(argc, argv, "hcUDSd:l:L:e:i:r:q:3:s:x:t:O:")) != -1) {
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switch (carg) {
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/* -------------------- */
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@ -516,6 +460,12 @@ int main(int argc, char **argv)
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options.g++;
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break;
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/* --------------------------------- */
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case 'O': /* set primer size */
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/* --------------------------------- */
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sscanf(optarg,"%d",&(options.primer_length));
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break;
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/* -------------------- */
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case 'c': /* sequences are circular */
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/* --------------------------------- */
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@ -601,7 +551,7 @@ int main(int argc, char **argv)
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/*TR: Added*/
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pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
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// setoktaxforspecificity (&pairs);
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@ -104,7 +104,7 @@ typedef struct {
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* on all sequences as a list of primer_t
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*/
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typedef struct {
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pprimer_t primers;
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pprimer_t primers;
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uint32_t size;
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} primercount_t, *pprimercount_t;
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@ -170,6 +170,8 @@ typedef struct {
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float yule;
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float quorumin;
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float quorumout;
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float bs;
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float bc;
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//
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// uint32_t taxsetcount;
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// uint32_t taxsetindex;
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@ -224,7 +226,7 @@ typedef struct {
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typedef struct {
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int32_t taxid;
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void *amptree;
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void *amptree;
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}taxontoamp_t, *ptaxontoamp_t;
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typedef struct {
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@ -40,7 +40,7 @@ int32_t counttaxon(int32_t taxid)
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taxoncount=0;
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return 0;
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}
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if ((taxid > 0) && ((!taxontree) || (!tfind((void*)((size_t)taxid),&taxontree,cmptaxon))))
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{
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@ -108,18 +108,21 @@ float taxonomycoverage(ppair_t pair, poptions_t options)
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counttaxon(-1);
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for (i=0; i < seqcount; i++)
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if (pair->pcr.amplifias[i].sequence->isexample)
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if (pair->pcr.amplifias[i].sequence->isexample
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&& pair->pcr.amplifias[i].sequence->ranktaxonid > 0 )
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incount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
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counttaxon(-1);
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for (i=0; i < seqcount; i++)
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if (!pair->pcr.amplifias[i].sequence->isexample)
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if (!pair->pcr.amplifias[i].sequence->isexample
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&& pair->pcr.amplifias[i].sequence->ranktaxonid)
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outcount = counttaxon(pair->pcr.amplifias[i].sequence->ranktaxonid);
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pair->intaxa=incount;
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pair->outtaxa=outcount;
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return (float)incount/options->intaxa;
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pair->bc=(float)incount/options->intaxa;
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return pair->bc;
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}
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@ -132,11 +135,11 @@ static int cmpamp(const void *ampf1, const void* ampf2)
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char cd2;
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int chd = 0;
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int len = 0;
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pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
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pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
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if (pampf1->strand != pampf2->strand)
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{
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incr = -1;
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@ -148,9 +151,9 @@ static int cmpamp(const void *ampf1, const void* ampf2)
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chd = 1;
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}
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}
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len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
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for (i = 0; i < len; i++, j += incr)
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{
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cd1 = pampf1->amplifia[i];
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@ -158,14 +161,14 @@ static int cmpamp(const void *ampf1, const void* ampf2)
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cd2 = ecoComplementChar(pampf2->amplifia[j]);
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else
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cd2 = pampf2->amplifia[j];
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if (cd1 < cd2) return chd ? 1: -1;
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if (cd2 < cd1) return chd ? -1: 1;
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}
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if (pampf1->length > pampf2->length) return chd ? -1: 1;
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if (pampf2->length > pampf1->length) return chd ? 1: -1;
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return 0;
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}
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@ -183,42 +186,48 @@ void taxonomyspecificity (ppair_t pair)
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void *ampftree = NULL;
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pamptotaxon_t pcurrentampf;
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pamptotaxon_t *ptmp;
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pamptotaxon_t ampfwithtaxtree = ECOMALLOC(sizeof(amptotaxon_t) * pair->pcr.ampcount,"Cannot allocate amplifia tree");
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for (i = 0; i < pair->pcr.ampcount; i++)
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{
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/*populate taxon ids tree against each unique amplifia
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i.e set of taxon ids for each amplifia*/
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ampfwithtaxtree[ampfindex].amplifia = pair->pcr.amplifias[i].amplifia;
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ampfwithtaxtree[ampfindex].strand = pair->pcr.amplifias[i].strand;
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ampfwithtaxtree[ampfindex].length = pair->pcr.amplifias[i].length;
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pcurrentampf = &fwithtaxtree[ampfindex];
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taxid = pair->pcr.amplifias[i].sequence->ranktaxonid;
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ptmp = tfind((const void*)pcurrentampf, &ftree, cmpamp);
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if (ptmp == NULL)
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if (pair->pcr.amplifias[i].sequence->isexample)
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{
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ampfwithtaxtree[ampfindex].amplifia = pair->pcr.amplifias[i].amplifia;
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ampfwithtaxtree[ampfindex].strand = pair->pcr.amplifias[i].strand;
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ampfwithtaxtree[ampfindex].length = pair->pcr.amplifias[i].length;
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pcurrentampf = &fwithtaxtree[ampfindex];
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tsearch((void*)pcurrentampf,&ftree,cmpamp);
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ampfindex++;
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}
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else
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pcurrentampf = *ptmp;
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if (tfind((void*)((size_t)taxid), &(pcurrentampf->taxontree), cmptaxon) == NULL)
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{
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pcurrentampf->taxoncount++;
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tsearch((void*)((size_t)taxid),&(pcurrentampf->taxontree),cmptaxon);
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taxid = pair->pcr.amplifias[i].sequence->ranktaxonid;
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ptmp = tfind((const void*)pcurrentampf, &ftree, cmpamp);
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if (ptmp == NULL)
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{
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pcurrentampf = &fwithtaxtree[ampfindex];
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tsearch((void*)pcurrentampf,&ftree,cmpamp);
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ampfindex++;
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}
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else
|
||||
pcurrentampf = *ptmp;
|
||||
|
||||
if (tfind((void*)((size_t)taxid), &(pcurrentampf->taxontree), cmptaxon) == NULL)
|
||||
{
|
||||
pcurrentampf->taxoncount++;
|
||||
tsearch((void*)((size_t)taxid),&(pcurrentampf->taxontree),cmptaxon);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
counttaxon(-1);
|
||||
for (i = 0; i < ampfindex; i++)
|
||||
{
|
||||
if (ampfwithtaxtree[i].taxoncount > 1)
|
||||
twalk(ampfwithtaxtree[i].taxontree, twalkaction);
|
||||
}
|
||||
|
||||
|
||||
pair->notwellidentifiedtaxa = counttaxon(-2);
|
||||
pair->bs = ((float)pair->intaxa - (float)pair->notwellidentifiedtaxa) / pair->intaxa;
|
||||
|
||||
ECOFREE (ampfwithtaxtree, "Free amplifia table");
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user