--- /dev/null
+/* calculate stats from results file using scalesws.c */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <limits.h>
+#include <math.h>
+
+#define MAX_LLEN 200
+
+#define LN_FACT 10.0
+
+#include "defs.h"
+#include "structs.h"
+#include "param.h"
+
+struct beststr {
+ int score; /* smith-waterman score */
+ int sscore; /* duplicate for compatibility with fasta */
+ double comp;
+ double H;
+ double zscore;
+ double escore;
+ int n1;
+#ifndef USE_FTELLO
+ long lseek; /* position in library file */
+#else
+ off_t lseek;
+#endif
+ int cont; /* offset into sequence */
+ int frame;
+ int lib;
+ char libstr[13];
+} *bbp, *bestptr, **bptr, *best;
+
+struct stat_str {
+ int score;
+ int n1;
+ double comp;
+ double H;
+};
+
+static struct db_str qtt = {0l, 0l, 0};
+
+char gstring2[MAX_STR]; /* string for label */
+char gstring3[MAX_STR];
+char hstring1[MAX_STR];
+
+FILE *outfd;
+
+int nbest; /* number of sequences better than bestcut in best */
+int bestcut=1; /* cut off for getting into MAXBEST */
+int bestfull;
+
+int dohist = 0;
+int zsflag = 1;
+int outtty=1;
+int llen=40;
+
+/* statistics functions */
+extern void
+process_hist(struct stat_str *sptr, int nstat, struct pstruct pst,
+ struct hist_str *hist, void **);
+extern void addhistz(double, struct hist_str *); /* scaleswn.c */
+void selectbestz(struct beststr **, int, int );
+
+extern double zs_to_E(double, int, int, long, struct db_str);
+extern double zs_to_Ec(double zs, long entries);
+
+extern double (*find_zp)(int score, int length, double comp, void *);
+
+void prhist(FILE *, struct mngmsg, struct pstruct, struct hist_str,
+ int, struct db_str, char *);
+
+int nshow=20, mshow=50, ashow= -1;
+double e_cut=10.0;
+
+main(argc, argv)
+ int argc; char **argv;
+{
+ FILE *fin;
+ char line[512];
+ int max, icol, iarg, i, qsfnum, lsfnum, n0, n1, s[3], frame;
+ double comp, H;
+ int idup, ndup, max_s;
+ char libstr[20], *bp;
+ char bin_file[80];
+ FILE *bout=NULL;
+ struct mngmsg m_msg; /* Message from host to manager */
+ struct pstruct pst;
+ struct stat_str *stats;
+ int nstats;
+ double zscor, mu, var;
+
+#if defined(UNIX)
+ outtty = isatty(1);
+#else
+ outtty = 1;
+#endif
+
+ if (argc < 2 ) {
+ fprintf(stderr," useage - res_stats -c col -r bin_file file\n");
+ exit(1);
+ }
+
+ m_msg.db.length = qtt.length = 0l;
+ m_msg.db.entries = m_msg.db.carry = qtt.entries = qtt.carry = 0;
+ m_msg.pstat_void = NULL;
+ m_msg.hist.hist_a = NULL;
+ m_msg.nohist = 0;
+ m_msg.markx = 0;
+
+ pst.n0 = 200; /* sensible dummy value */
+ pst.zsflag = 1;
+ pst.dnaseq = 0;
+ pst.histint = 2;
+
+ bin_file[0]='\0';
+ icol = 1;
+ iarg = 1;
+ ndup = 1;
+ while (1) {
+ if (argv[iarg][0]=='-' && argv[iarg][1]=='c') {
+ sscanf(argv[iarg+1],"%d",&icol);
+ iarg += 2;
+ }
+ else if (argv[iarg][0]=='-' && argv[iarg][1]=='r') {
+ strncpy(bin_file,argv[iarg+1],sizeof(bin_file));
+ iarg += 2;
+ }
+ else if (argv[iarg][0]=='-' && argv[iarg][1]=='z') {
+ sscanf(argv[iarg+1],"%d",&pst.zsflag);
+ iarg += 2;
+ }
+ else if (argv[iarg][0]=='-' && argv[iarg][1]=='n') {
+ pst.dnaseq = 1;
+ iarg += 1;
+ }
+ else if (argv[iarg][0]=='-' && argv[iarg][1]=='s') {
+ sscanf(argv[iarg+1],"%d",&ndup);
+ iarg += 2;
+ }
+ else if (argv[iarg][0]=='-' && argv[iarg][1]=='q') {
+ outtty = 0;
+ iarg += 1;
+ }
+ else break;
+ }
+
+ icol--;
+
+ if ((fin=fopen(argv[iarg],"r"))==NULL) {
+ fprintf(stderr," cannot open %s\n",argv[1]);
+ exit(1);
+ }
+
+ if (bin_file[0]!='\0' && ((bout=fopen(bin_file,"w"))==NULL)) {
+ fprintf(stderr,"cannot open %s for output\n",bin_file);
+ }
+
+ if ((stats =
+ (struct stat_str *)malloc((MAXSTATS)*sizeof(struct stat_str)))==NULL)
+ s_abort ("Cannot allocate stats struct","");
+ nstats = 0;
+
+ initbest(MAXBEST+1); /* +1 required for select() */
+
+ for (nbest=0; nbest<MAXBEST+1; nbest++)
+ bptr[nbest] = &best[nbest];
+ bptr++; best++;
+ best[-1].score= BIGNUM;
+
+ nbest = 0;
+
+ pst.Lambda=0.232;
+ pst.K = 0.11;
+ pst.H = 0.34;
+
+ /* read the best scores from the results file */
+
+ max_s = -1;
+ idup = 0;
+
+ /* get first line with sequence length */
+ fgets(line,sizeof(line),fin);
+ sscanf(line,"%d",&n0);
+ if (n0 > 0) pst.n0 = n0;
+
+ while (fgets(line,sizeof(line),fin)!=NULL) {
+ if (line[0]=='/' && line[1]=='*') {
+ fputs(line,stdout);
+ strncpy(gstring2,line,sizeof(gstring2));
+ if ((bp=strchr(gstring2,'\n'))!=NULL) *bp = '\0';
+ break;
+ }
+ if (line[0]==';') {
+ if ((bp=strchr(line,'|'))!=NULL) qsfnum = atoi(bp+1);
+ else continue;
+ if ((bp=strchr(line,'('))!=NULL) {
+ n0 = atoi(bp+1);
+ pst.n0 = n0;
+ }
+ else {
+ fprintf(stderr, "cannot find n0:\n %s\n",line);
+ continue;
+ }
+ }
+ else {
+ sscanf(line,"%s %d %d %d %lf %lf %d %d %d",
+ libstr,&lsfnum,&n1,&frame,&comp, &H, &s[0],&s[1],&s[2]);
+ if (lsfnum==0 && n1==0) {
+ fputs(line,stderr);
+ continue;
+ }
+ if (n1 < 10 || s[icol]<=0) fputs(line,stderr);
+ idup++;
+
+ if (s[icol] > max_s) max_s = s[icol];
+ if (idup < ndup) continue;
+
+ m_msg.db.entries++;
+ m_msg.db.length += n1;
+
+ if (dohist) addhistz(zscor=(*find_zp)(max_s,n1,comp,m_msg.pstat_void),
+ &m_msg.hist);
+ else zscor = (double)max_s;
+
+ if (nstats < MAXSTATS) {
+ stats[nstats].n1 = n1;
+ stats[nstats].comp = comp;
+ stats[nstats].H = H;
+ stats[nstats++].score = max_s;
+ }
+
+ else if (!dohist) {
+ /* do_bout(bout,stats,nstats); */
+ process_hist(stats,nstats,pst,&m_msg.hist, &m_msg.pstat_void);
+ for (i=0; i<nbest; i++)
+ bptr[i]->zscore =
+ (*find_zp)(bptr[i]->score,bptr[i]->n1,bptr[i]->comp,
+ m_msg.pstat_void);
+ dohist = 1;
+ }
+
+ if (dohist) {
+ zscor =(*find_zp)(max_s,n1,comp,m_msg.pstat_void);
+ addhistz(zscor,&m_msg.hist);
+ }
+ else zscor = (double)max_s;
+
+ if (nbest >= MAXBEST) {
+ bestfull = nbest-MAXBEST/4;
+ selectz(bestfull-1,nbest);
+ bestcut = (int)(bptr[bestfull-1]->zscore+0.5);
+ nbest = bestfull;
+ }
+ bestptr = bptr[nbest];
+ bestptr->score = max_s;
+ bestptr->sscore = max_s;
+ bestptr->n1 = n1;
+ bestptr->comp = comp;
+ bestptr->H = H;
+ bestptr->lib = lsfnum;
+ bestptr->zscore = zscor;
+ strncpy(bestptr->libstr,libstr,12);
+ bestptr->libstr[12]='\0';
+ nbest++;
+
+ max_s = -1;
+ idup = 0;
+ }
+ } /* done with reading results */
+
+ if (!dohist) {
+ if (nbest < 20) {
+ zsflag = 0;
+ }
+ else {
+ /* do_bout(bout,stats,nstats); */
+ process_hist(stats,nstats,pst,&m_msg.hist,&m_msg.pstat_void);
+ for (i=0; i<nbest; i++)
+ bptr[i]->zscore =
+ (*find_zp)(bptr[i]->score,bptr[i]->n1,bptr[i]->comp,m_msg.pstat_void);
+ dohist = 1;
+ }
+ }
+
+ printf(" using n0: %d\n",pst.n0);
+
+ /* print histogram, statistics */
+
+ m_msg.nbr_seq = m_msg.db.entries;
+ pst.zdb_size = m_msg.db.entries;
+ /* get_param(&pst, gstring2,gstring3); */
+
+ prhist(stdout,m_msg,pst,m_msg.hist,nstats,m_msg.db,gstring2);
+
+ if (!zsflag) sortbest();
+ else {
+ sortbestz(bptr,nbest);
+ for (i=0; i<nbest; i++)
+ bptr[i]->escore = zs_to_E(bptr[i]->zscore,bptr[i]->n1,pst.dnaseq,
+ pst.zdb_size, m_msg.db);
+ }
+
+ outfd = stdout;
+ showbest(m_msg.db); /* display best matches */
+}
+
+initbest(nbest) /* allocate arrays for best sort */
+ int nbest;
+{
+
+ if ((best=(struct beststr *)calloc((size_t)nbest,sizeof(struct beststr)))
+ == NULL) {fprintf(stderr,"cannot allocate best struct\n"); exit(1);}
+ if ((bptr=(struct beststr **)calloc((size_t)nbest,sizeof(struct beststr *)))
+ == NULL) {fprintf(stderr,"cannot allocate bptr\n"); exit(1);}
+}
+
+void
+prhist(FILE *fd, struct mngmsg m_msg,
+ struct pstruct pst,
+ struct hist_str hist,
+ int nstats,
+ struct db_str ntt,
+ char *gstring2)
+{
+ int i,j,hl,hll, el, ell, ev;
+ char hline[80], pch, *bp;
+ int mh1, mht;
+ int maxval, maxvalt, dotsiz, ddotsiz,doinset;
+ double cur_e, prev_e, f_int;
+ double max_dev, x_tmp;
+ double db_tt;
+ int n_chi_sq, cum_hl, max_i;
+
+
+ fprintf(fd,"\n");
+
+ if (pst.zsflag < 0 || nstats <= 10) {
+ fprintf(fd, "%7ld residues in %5ld sequences\n", ntt.length,ntt.entries);
+ fprintf(fd,"\n%s\n",gstring2);
+ return;
+ }
+
+ max_dev = 0.0;
+ mh1 = hist.maxh-1;
+ mht = (3*hist.maxh-3)/4 - 1;
+
+ if (!m_msg.nohist && mh1 > 0) {
+ for (i=0,maxval=0,maxvalt=0; i<hist.maxh; i++) {
+ if (hist.hist_a[i] > maxval) maxval = hist.hist_a[i];
+ if (i >= mht && hist.hist_a[i]>maxvalt) maxvalt = hist.hist_a[i];
+ }
+ n_chi_sq = 0;
+ cum_hl = -hist.hist_a[0];
+ dotsiz = (maxval-1)/60+1;
+ ddotsiz = (maxvalt-1)/50+1;
+ doinset = (ddotsiz < dotsiz && dotsiz > 2);
+
+ if (pst.zsflag>=0)
+ fprintf(fd," opt E()\n");
+ else
+ fprintf(fd," opt\n");
+
+ prev_e = zs_to_Ec((double)(hist.min_hist-hist.histint/2),hist.entries);
+ for (i=0; i<=mh1; i++) {
+ pch = (i==mh1) ? '>' : ' ';
+ pch = (i==0) ? '<' : pch;
+ hll = hl = hist.hist_a[i];
+ if (pst.zsflag>=0) {
+ cum_hl += hl;
+ f_int = (double)(i*hist.histint+hist.min_hist)+(double)hist.histint/2.0;
+ cur_e = (double)zs_to_Ec(f_int,hist.entries);
+ ev = el = ell = (int)(cur_e - prev_e + 0.5);
+ if (hl > 0 && i > 5 && i < (90-hist.min_hist)/hist.histint) {
+ x_tmp = fabs(cum_hl - cur_e);
+ if ( x_tmp > max_dev) {
+ max_dev = x_tmp;
+ max_i = i;
+ }
+ n_chi_sq++;
+ }
+ if ((el=(el+dotsiz-1)/dotsiz) > 60) el = 60;
+ if ((ell=(ell+ddotsiz-1)/ddotsiz) > 40) ell = 40;
+ fprintf(fd,"%c%3d %5d %5d:",
+ pch,(i<mh1)?(i)*hist.histint+hist.min_hist :
+ mh1*hist.histint+hist.min_hist,hl,ev);
+ }
+ else fprintf(fd,"%c%3d %5d :",
+ pch,(i<mh1)?(i)*hist.histint+hist.min_hist :
+ mh1*hist.histint+hist.min_hist,hl);
+
+ if ((hl=(hl+dotsiz-1)/dotsiz) > 60) hl = 60;
+ if ((hll=(hll+ddotsiz-1)/ddotsiz) > 40) hll = 40;
+ for (j=0; j<hl; j++) hline[j]='=';
+ if (pst.zsflag>=0) {
+ if (el <= hl ) {
+ if (el > 0) hline[el-1]='*';
+ hline[hl]='\0';
+ }
+ else {
+ for (j = hl; j < el; j++) hline[j]=' ';
+ hline[el-1]='*';
+ hline[hl=el]='\0';
+ }
+ }
+ else hline[hl] = 0;
+ if (i==1) {
+ for (j=hl; j<10; j++) hline[j]=' ';
+ sprintf(&hline[10]," one = represents %d library sequences",dotsiz);
+ }
+ if (doinset && i == mht-2) {
+ for (j = hl; j < 10; j++) hline[j]=' ';
+ sprintf(&hline[10]," inset = represents %d library sequences",ddotsiz);
+ }
+ if (i >= mht&& doinset ) {
+ for (j = hl; j < 10; j++) hline[j]=' ';
+ hline[10]=':';
+ for (j = 11; j<11+hll; j++) hline[j]='=';
+ hline[11+hll]='\0';
+ if (pst.zsflag>=0) {
+ if (ell <= hll) hline[10+ell]='*';
+ else {
+ for (j = 11+hll; j < 10+ell; j++) hline[j]=' ';
+ hline[10+ell] = '*';
+ hline[11+ell] = '\0';
+ }
+ }
+ }
+
+ fprintf(fd,"%s\n",hline);
+ prev_e = cur_e;
+ }
+ }
+
+ if (ntt.carry==0) {
+ fprintf(fd, "%7ld residues in %5ld sequences\n", ntt.length, ntt.entries);
+ }
+ else {
+ db_tt = (double)ntt.carry*(double)LONG_MAX + (double)ntt.length;
+ fprintf(fd, "%.0f residues in %5ld library sequences\n", db_tt, ntt.entries);
+ }
+
+ if (pst.zsflag>=0) {
+ if (MAXSTATS < hist.entries)
+ fprintf(fd," statistics extrapolated from %d to %ld sequences\n",
+ MAXSTATS,hist.entries);
+ /* summ_stats(stat_info); */
+ fprintf(fd," %s\n",hist.stat_info);
+ if (!m_msg.nohist && cum_hl > 0)
+ fprintf(fd," Kolmogorov-Smirnov statistic: %6.4f (N=%d) at %3d\n",
+ max_dev/(double)cum_hl, n_chi_sq,max_i*hist.histint+hist.min_hist);
+ if (m_msg.markx & MX_M10FORM) {
+ while ((bp=strchr(hist.stat_info,'\n'))!=NULL) *bp=' ';
+ if (cum_hl <= 0) cum_hl = -1;
+ sprintf(hstring1,"; mp_extrap: %d %ld\n; mp_stats: %s\n; mp_KS: %6.4f (N=%d) at %3d\n",
+ MAXSTATS,hist.entries,hist.stat_info,max_dev/(double)cum_hl, n_chi_sq,max_i*hist.histint+hist.min_hist);
+ }
+ }
+ fprintf(fd,"\n%s\n",gstring2);
+ fflush(fd);
+}
+
+showbest(struct db_str ntt)
+ {
+ int ib, istart, istop;
+ char bline[200], fmt[40], pad[200];
+ char rline[20];
+ int ntmp;
+ int lcont, ccont, loff;
+ int hcutoff;
+
+ sprintf(fmt,"%%-%ds (%%3d)",llen-10);
+
+ nshow = min(20,nbest);
+ mshow = min(20,nbest);
+
+ if (outtty) {
+ printf(" How many scores would you like to see? [%d] ",nshow);
+ fflush(stdout);
+ if (fgets(rline,sizeof(rline),stdin)==NULL) exit(0);
+ if (rline[0]!='\n' && rline[0]!=0) sscanf(rline,"%d",&nshow);
+ if (nshow<=0) nshow = min(20,nbest);
+ }
+ else nshow=mshow;
+
+ memset(pad,' ',llen-10);
+ pad[llen-31]='\0';
+ if (zsflag)
+ fprintf(outfd,"The best scores are:%s s-w Z-score E(%ld)\n",pad,ntt.entries);
+ else
+ fprintf(outfd,"The best scores are:%s s-w\n",pad);
+
+ if (outfd != stdout)
+ if (zsflag)
+ fprintf(stdout,"The best scores are:%s s-w Z-score E(%ld)\n",pad,ntt.entries);
+ else
+ fprintf(stdout,"The best scores are:%s s-w\n",pad);
+
+ istart = 0;
+ l1: istop = min(nbest,nshow);
+ for (ib=istart; ib<istop; ib++) {
+ bbp = bptr[ib];
+
+ if (!outtty && zsflag && bbp->escore > e_cut) {
+ nshow = ib;
+ goto done;
+ }
+
+ sprintf(bline,"%-12s %d",bbp->libstr,bbp->lib);
+ bline[13]='\0';
+
+ fprintf(outfd,fmt,bline,bbp->n1);
+
+ if (zsflag)
+ fprintf(outfd,"%4d %4.1f %6.2g\n",
+ bbp->score,bbp->zscore,
+ bbp->escore);
+ else
+ fprintf(outfd,"%4d\n",bbp->score);
+
+ if (outfd!=stdout) {
+ fprintf(stdout,fmt,bline,bbp->n1);
+ if (zsflag)
+ printf("%4d %4.1f %6.2g\n",
+ bbp->score,bbp->zscore,
+ bbp->escore);
+ else
+ printf("%4d\n",bbp->score);
+ }
+ }
+
+ fflush(outfd); if (outfd!=stdout) fflush(stdout);
+
+ if (outtty) {
+ printf(" More scores? [0] ");
+ fflush(stdout);
+ if (fgets(rline,sizeof(rline),stdin)==NULL) exit(0);
+ ntmp = 0;
+ if (rline[0]!='\n' && rline[0]!=0) sscanf(rline,"%d",&ntmp);
+ if (ntmp<=0) ntmp = 0;
+ if (ntmp>0) {
+ istart = istop;
+ nshow += ntmp;
+ mshow += ntmp;
+ goto l1;
+ }
+ }
+ else if (zsflag && bbp->escore < e_cut) {
+ istart=istop;
+ nshow += 10;
+ goto l1;
+ }
+
+ done:
+ if (outfd!=stdout) fprintf(outfd,"\n");
+}
+
+selectz(k,n) /* k is rank in array */
+ int k,n;
+{
+ int t, i, j, l, r;
+ double v;
+ struct beststr *tmptr;
+
+ l=0; r=n-1;
+
+ while ( r > l ) {
+ i = l-1;
+ j = r;
+ v = bptr[r]->zscore;
+ do {
+ while (bptr[++i]->zscore > v ) ;
+ while (bptr[--j]->zscore < v ) ;
+ tmptr = bptr[i]; bptr[i]=bptr[j]; bptr[j]=tmptr;
+ } while (j > i);
+ bptr[j]=bptr[i]; bptr[i]=bptr[r]; bptr[r]=tmptr;
+ if (i>=k) r = i-1;
+ if (i<=k) l = i+1;
+ }
+}
+
+sortbest()
+{
+ int cmps(), cmp1(), cmpa(), cmpz();
+ ksort(bptr,nbest,cmps);
+}
+
+sortbeste()
+{
+ int cmpe();
+ ksort(bptr,nbest,cmpe);
+}
+
+sortbestz()
+{
+ int cmpz();
+ ksort(bptr,nbest,cmpz);
+}
+
+cmps(ptr1,ptr2)
+ struct beststr *ptr1, *ptr2;
+{
+ if (ptr1->score < ptr2->score) return (1);
+ else if (ptr1->score > ptr2->score) return (-1);
+ else return (0);
+}
+
+cmpe(ptr1,ptr2)
+ struct beststr *ptr1, *ptr2;
+{
+ if (ptr1->escore < ptr2->escore) return (-1);
+ else if (ptr1->escore > ptr2->escore) return (1);
+ else return (0);
+}
+
+cmpz(ptr1,ptr2)
+ struct beststr *ptr1, *ptr2;
+{
+ if (ptr1->zscore < ptr2->zscore) return (1);
+ else if (ptr1->zscore > ptr2->zscore) return (-1);
+ else return (0);
+}
+
+ksort(v,n,comp)
+ char *v[]; int n, (*comp)();
+{
+ int gap, i, j;
+ char *tmp;
+
+ for (gap=n/2; gap>0; gap/=2)
+ for (i=gap; i<n; i++)
+ for (j=i-gap; j>=0; j -= gap) {
+ if ((*comp)(v[j],v[j+gap]) <=0)
+ break;
+ tmp = v[j]; v[j]=v[j+gap]; v[j+gap]=tmp;
+ }
+}
+
+/*
+do_bout(FILE *bout,struct stat_str **bptr, int nbest)
+{
+ int i, min_hist, max_hist;
+ double mu, var;
+
+ if (bout==NULL) return;
+
+ inithist();
+ for (i = 0; i<nbest; i++)
+ addhist(bptr[i]->score,bptr[i]->n1);
+
+ for (i=0; i<MAX_LLEN; i++)
+ if (llen_hist[i]>0) {
+ min_hist=i;
+ break;
+ }
+
+ for (i=MAX_LLEN-1; i>=0; i--)
+ if (llen_hist[i]>0) {
+ max_hist=i;
+ break;
+ }
+
+ for (i=min_hist; i<=max_hist; i++) {
+ mu=(double)score_sums[i]/(double)llen_hist[i];
+ if (llen_hist[i]>1) {
+ var = ((double)score2_sums[i]-(double)llen_hist[i]*mu*mu)/
+ (double)(llen_hist[i]-1);
+
+ fprintf(bout,"%d\t%d\t%.1f\t%.1f\t%.1f\t%.4f\t%.4f\n",
+ i,llen_hist[i],exp(((double)(i))/LN_FACT),
+ score_sums[i],score2_sums[i],mu,var);
+ }
+ }
+ free_hist();
+ fclose(bout);
+}
+*/
+
+s_abort()
+{
+ exit(1);
+}
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