a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/hg/sage/createSageSummary.c src/hg/sage/createSageSummary.c index ebd6ae1..2b6ba8a 100644 --- src/hg/sage/createSageSummary.c +++ src/hg/sage/createSageSummary.c @@ -1,257 +1,256 @@ /** \page createSageSummary.doxp createSageSummary Doc Page

createSageSummary takes the tagList file (i.e. SAGEmap_ug_tag-rel-Nla3-Hs) and the file produced by the createArraysForTags.pl script in ~/cc/sage/sage/extr (i.e. tagExpArrays.tab). The output is a file of sage records from sage.h which have precalculate./createSageSummary SAGEmap_ug_tag-rel-Nla3-Hs tagExpArrays.tab out.tabd unigene entries mean,median, and stdev of tag counts for each experiment. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "sage.h" #include "sageCounts.h" -static char const rcsid[] = "$Id: createSageSummary.c,v 1.3 2008/09/03 19:21:18 markd Exp $"; struct sage *createNewSage(int numExp) { struct sage *sg = NULL; AllocVar(sg); sg->numExps = numExp; sg->exps = needMem(sizeof(int) * sg->numExps); sg->meds = needMem(sizeof(float) * sg->numExps); sg->aves = needMem(sizeof(float) * sg->numExps); sg->stdevs = needMem(sizeof(float) * sg->numExps); return sg; } struct sage *loadSageTags(char *fileName, int numExps) { struct sage *sgList=NULL, *sg=NULL; char *words[3]; struct lineFile *lf = lineFileOpen(fileName, TRUE); while(lineFileNextRow(lf, words,3)) { if(sg == NULL || sg->uni != atoi(words[0])) { if(sg != NULL) slSafeAddHead(&sgList,sg); sg = createNewSage(numExps); sg->uni = atoi(words[0]); snprintf(sg->gb, sizeof(sg->gb), "unknown"); snprintf(sg->gi, sizeof(sg->gb), "unknown"); sg->description = cloneString(words[1]); sg->numTags =1; assert(strlen(words[2]) <= 10); sg->tags = needMem(sizeof(char*) * 1); sg->tags[0] = needMem(sizeof(char) * 11); strcpy(sg->tags[0],words[2]); } else { sg->tags = needMoreMem(sg->tags, (sg->numTags*sizeof(char*)), ((sg->numTags+1)*sizeof(char*))); sg->tags[sg->numTags] = needMem(sizeof(char) * 11); strcpy(sg->tags[sg->numTags],words[2]); sg->numTags++; } } return(sgList); /*for(sg=sgList; sg != NULL; sg = sg->next) { sageTabOut(sg,stdout); }*/ } void putTic() { printf("."); fflush(stdout); } void loadTagHash(struct hash *h, struct sageCounts *scList) { struct sageCounts *sc =NULL; int count=0; for(sc=scList;sc!=NULL;sc=sc->next) { if(count++ % 10000 == 0) { putTic(); } hashAddUnique(h,sc->tag,sc); } printf("\tDone.\n"); } struct sortable { struct sortable *next; int val; }; int compSortable(const void *e1, const void *e2) { const struct sortable *v1 = *((struct sortable**)e1); const struct sortable *v2 = *((struct sortable**)e2); return v1->val - v2->val; } /* if N is odd, the median is the element in the middle of the rearranged sequence, and if N is even, the median is the average of the two elements in the middle of the rearranged sequence. */ float scMedian(struct sageCounts *scList, int index) { struct sageCounts *sc = NULL; struct sortable *s=NULL, *sList = NULL, *next = NULL, *s2 = NULL; boolean odd = slCount(scList) %2; int half = slCount(scList)/2; float median = -1; for(sc = scList; sc != NULL; sc = sc->next) { AllocVar(s); s->val = sc->expCounts[index]; slAddHead(&sList,s); } slSort(&sList,compSortable); if(odd) { s = slElementFromIx(sList,half); if(s != NULL) median = s->val; } else { s = slElementFromIx(sList,half); s2 = slElementFromIx(sList,half-1); if(s != NULL && s2 != NULL) median = (float)((float)s->val + (float)s2->val)/2; } for(s=sList; s != NULL; s = next) { next = s->next; freez(&s); } return median; } float scAverage(struct sageCounts *scList, int index) { struct sageCounts *sc = NULL; int sum=0,count=0; if(slCount(scList)==0) return -1.0; for(sc=scList;sc!=NULL;sc=sc->next) { count++; sum+= sc->expCounts[index]; } return (float)sum/count; } float scStdev(struct sageCounts *scList, int index, float ave) { struct sageCounts *sc = NULL; float sum =0; int count =0; if(ave == -1) return -1; if(slCount(scList)==0) return -1.0; if(slCount(scList)==1) return 0.0; for(sc=scList;sc!=NULL;sc=sc->next) { sum += (sc->expCounts[index]-ave) * (sc->expCounts[index]-ave); count++; } return (float) sqrt(sum/(count-1)); } void printListVals(struct sageCounts *scList, int index) { struct sageCounts *sc = NULL; struct sortable *s=NULL, *sList = NULL, *next = NULL; for(sc = scList; sc != NULL; sc = sc->next) { AllocVar(s); s->val = sc->expCounts[index]; slAddHead(&sList,s); } slSort(&sList,compSortable); for(s = sList; s!= NULL; s=s->next) uglyf("%d,",s->val); uglyf("\n"); for(s=sList; s != NULL; s = next) { next = s->next; freez(&s); } } void createSageSummary(char *tagList, char *tagCounts, char *outFile) { struct sage *sgList = NULL,*sg = NULL; struct sageCounts *scList = NULL, *sc; struct hash *scHash = newHash(16); FILE *out = mustOpen(outFile,"w"); int i,count=0; printf("Loading tagCounts.\n"); scList = sageCountsLoadAll(tagCounts); printf("Loading SageTags.\n"); sgList = loadSageTags(tagList, scList->numExps); printf("Inserting scList into hash, %d elements.\n",slCount(scList)); loadTagHash(scHash,scList); printf("Calculating avgs and stdevs"); fflush(stdout); for(sg=sgList; sg != NULL; sg=sg->next) { if(count++ %1000 == 0) putTic(); scList = NULL; for(i=0;inumTags;i++) { sc = hashFindVal(scHash,sg->tags[i]); if(sc != NULL) slSafeAddHead(&scList,sc); } for(i=0; inumExps; i++) { sg->exps[i] =i; if(slCount(scList) > 3) { #ifdef BOGUS int q = 2+2; #endif } sg->meds[i] = scMedian(scList,i); sg->aves[i] = scAverage(scList, i); sg->stdevs[i] = scStdev(scList, i, sg->aves[i]); } sageTabOut(sg,out); fflush(out); } carefulClose(&out); printf("\tDone.\n"); } void usage() { errAbort("usage:\n\tcreateSageSummary \n"); } int main(int argc, char *argv[]) { if(argc != 4) usage(); createSageSummary(argv[1], argv[2], argv[3]); return 0; }