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#include <ncoils.h>
#include <string.h>
/* Copyright (c) 2002 Robert B. Russell
* EMBL, Meyerhofstrasse 1, 69917 Heidelberg, Germany
* Email: russell@embl.de
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
/* Rob Russell's attempt to make a COILS program */
#ifndef __PKGDATADIR__
#define __PKGDATADIR__ ""
#endif
int main(int argc, char *argv[]) {
int i,j;
int verb;
int window,pt;
int which,weighted;
int nseq;
int t,tc;
int seqlen = 0;
int mode;
int min_seg;
#define HEPTFILELENGTH 1000
char heptfile[HEPTFILELENGTH];
char *buff;
static char *env;
char *seq = NULL;
char *title,*ident;
float min_P;
struct hept_pref *h;
FILE *MAT;
/* defaults */
window = 21;
weighted = 0;
verb = 0;
mode = 0; /* 0 = column mode, 1 = fasta, 2 = concise */
min_P = 0.5;
if((env=getenv("COILSDIR"))==NULL) env = __PKGDATADIR__;
if( env[0] == 0 ){ // empty string
fprintf(stderr,"error: environment variable COILSDIR must be set\n");
exit(-1);
}
strncpy(&heptfile[0],env,HEPTFILELENGTH-1-8); // -1 for terminal 0, 8 for "/new.mat"
strcpy(&heptfile[strlen(heptfile)],"/new.mat");
for(i=1; i<argc; ++i) {
if(argv[i][0]!='-') exit_error( env );
if(strcmp(&argv[i][1],"m")==0) {
if((i+1)>=argc) exit_error( env );
strncpy(&heptfile[0],argv[i+1],HEPTFILELENGTH-1);
i++;
} else if(strcmp(&argv[i][1],"win")==0) {
if((i+1)>=argc) exit_error( env );
sscanf(argv[i+1],"%d",&window);
i++;
} else if(strcmp(&argv[i][1],"c")==0) {
mode=2;
} else if(strcmp(&argv[i][1],"min_seg")==0) {
if((i+1)>=argc) exit_error( env );
sscanf(argv[i+1],"%d",&min_seg);
i++;
} else if(strcmp(&argv[i][1],"c")==0) {
mode=2;
} else if((strcmp(&argv[i][1],"f")==0) || (strcmp(&argv[i][1],"fasta")==0)) {
mode=1;
} else if((strcmp(&argv[i][1],"min_P")==0)) {
if((i+1)>=argc) exit_error( env );
sscanf(argv[i+1],"%f",&min_P);
i++;
} else if(strcmp(&argv[i][1],"help")==0) {
exit_error( env );
} else if(strcmp(&argv[i][1],"w")==0) {
weighted=1;
} else if(strcmp(&argv[i][1],"V")==0 || strcmp(&argv[i][1],"v")==0) {
verb=1;
} else {
fprintf(stderr," can't understand flag/field %s\n",argv[i]);
exit_error( env );
}
}
if(verb) printf("Matrix file is %s\n",heptfile);
/* Read in matrix */
if((MAT=fopen(heptfile,"r"))==NULL) {
fprintf(stderr,"Error reading %s\n",heptfile);
exit(-1);
}
h = read_matrix(MAT);
if(verb) {
for(i=0; i<strlen(AAs); ++i) if(AAs[i]!='_') {
pt=(int)(AAs[i]-'A');
printf("AA %c %4.2f %4.2f %4.2f %4.2f %4.2f %4.2f %4.2f\n",AAs[i],
h->m[pt][0],h->m[pt][1],h->m[pt][2],h->m[pt][3],h->m[pt][4],
h->m[pt][5],h->m[pt][6]);
}
for(i=0; i<h->n; ++i) {
printf("Window %4d %1d %f %f %f %f %f\n",
h->f[i].win,h->f[i].w,h->f[i].m_cc,h->f[i].sd_cc,h->f[i].m_g,h->f[i].sd_g,h->f[i].sc);
}
}
/* See if there is a file for our chosen window length/weight scheme */
which = -1;
for(i=0; i<h->n; ++i) {
if((h->f[i].win == window) && (h->f[i].w == weighted)) { /* match */
if(verb) printf("Found fitting data for win %4d w %d\n",window,weighted);
which = i;
}
}
/* Read in a sequence from the standard input */
nseq = 0;
ident = (char*) malloc(100000*sizeof(char));
title = (char*) malloc(100000*sizeof(char));
buff = (char*) malloc(100000*sizeof(char));
t = 0;
tc = 0;
while(fgets(buff,99999,stdin)!=NULL) {
/* There is a memory problem - the matrix data gets corrupted under OSF after this fgets */
for(i=0; i<strlen(buff); ++i) if(buff[i]=='\n' || buff[i]=='\r') buff[i]='\0';
if(buff[0]=='>') {
if(nseq>0) {
pred_coils(seq,ident,title,h,window,which,weighted,mode,min_P,&t,&tc,min_seg);
free(seq);
}
seqlen = 0;
i=1;
while((buff[i]!=' ') && (buff[i]!='\0') && (buff[i]!='\n') && (buff[i]!='\r')) { ident[i-1]=buff[i]; i++; }
ident[i-1]='\0';
i++; j=0;
seq = (char*)malloc(sizeof(char));
seq[0]='\0';
while(buff[i]!='\n' && buff[i]!='\0' && buff[i]!='\r') {
title[j]=buff[i]; i++;
j++;
}
title[j]='\0';
nseq++;
} else {
/* printf("Adding |%s| to |%s| = \n",buff,seq); */
seq=(char*)realloc(seq,(seqlen+strlen(buff)+1)*sizeof(char));
if (NULL == seq) {
fprintf(stderr,"Could not allocate memory.\n");
exit(-1);
}
strcpy(&seq[seqlen],buff);
seqlen=strlen(seq);
/* printf(" |%s|\n",seq); */
}
}
if(nseq>0) {
pred_coils(seq,ident,title,h,window,which,weighted,mode,min_P,&t,&tc,min_seg);
free(seq);
}
if( verb ) fprintf(stderr,"%8d sequences %8d aas %8d in coil\n",nseq,t,tc);
free(title); free(ident);
exit(0);
}
void exit_error( const char* __coilsdir ) {
fprintf(stderr,"format: ncoils [options] < [sequence file]\n");
fprintf(stderr," -f or -fasta [fasta output - coils as 'x', like '-x' in seg]\n");
fprintf(stderr," -c [concise mode - which sequences have any coils (and how many)]\n");
fprintf(stderr," -min_seg <int> [for concise mode - only report sequence if >= min coil segments]\n");
fprintf(stderr," -min_P <float> [minimum P to define coil segment; DEFAULT = 0.5]\n");
fprintf(stderr," -win <int> [window size; DEFAULT = 21]\n");
fprintf(stderr," -w [weight heptad positions a&d the same as b,c,e,f,g]\n");
fprintf(stderr," -v [verbose/debug mode - print extra junk]\n");
fprintf(stderr,"Effective COILSDIR: %s\n", __coilsdir );
fprintf(stderr,"\n");
fprintf(stderr,"NCOILS, Rob Russell and Andrei Lupas, 1999\n");
fprintf(stderr," based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164\n");
fprintf(stderr," Copyright (C) 1999 Robert B. Russell\n");
fprintf(stderr," NCOILS comes with ABSOLUTELY NO WARRANTY; for details see the file LICENSE\n");
fprintf(stderr," This is free software, and you are welcome to redistribute it\n");
fprintf(stderr," under certain conditions; see LICENSE for details\n");
exit(-1);
}
void pred_coils(char *seq,char *ident,char *title,struct hept_pref *h,int win, int which, int weighted,int mode, float min_P, int *t, int *tc, int min_seg) {
int i,j;
int len,pos,aa_pt;
int total_coil_segments;
int are_there_coils;
float actual_win;
float this_score,Gg,Gcc,power;
float t1,t2,t3,t4;
float *score;
float *P;
char *hept_seq;
len=strlen(seq);
score = (float*)malloc(len*sizeof(float));
P = (float*)malloc(len*sizeof(float));
hept_seq = (char*)malloc(len*sizeof(char));
/* printf("Sequence is %s length is %d\n",seq,len); */
for(i=0; i<len; ++i) { P[i]=0.0; score[i] = 0.0; hept_seq[i] = 'x'; }
for(i=0; i<(len-win+1); ++i) {
this_score = 1.0;
actual_win=0.0;
for(j=0; ((j<win) && ((i+j)<len)); ++j) {
aa_pt = (int)(seq[i+j]-'A');
if((aa_pt>=0) && (aa_pt<26) && (AAs[aa_pt]!='_')) {
pos = j%7; /* where are we in the heptad? pos modulus 7 */
/* printf("AA %c in hept %c %7.5f\n",seq[i+j],('a'+pos),h->m[aa_pt][pos]); */
if(weighted && (pos==0 || pos==3)) { power = 2.5; }
else { power = 1.0; }
actual_win+=power;
if(h->m[aa_pt][pos]!=-1) {
this_score*=pow(h->m[aa_pt][pos],power);
} else {
this_score*=pow(h->smallest,power);
}
}
}
if(actual_win>0) {
this_score = pow(this_score,(1/(float)actual_win));
} else {
this_score = 0;
}
for(j=0; ((j<win) && ((i+j)<len)); ++j) {
aa_pt = (int)(seq[i+j]-'A');
if((aa_pt>=0) && (aa_pt<26) && (AAs[aa_pt]!='_')) {
pos = j%7; /* where are we in the heptad? pos modulus 7 */
if(this_score>score[i+j]) { score[i+j]=this_score; hept_seq[i+j]='a'+pos; }
}
}
}
if(mode==1) {
printf(">%s %s\n",ident,title);
}
are_there_coils=0;
total_coil_segments=0;
for(i=0; i<len; ++i) {
/* Calculate P */
t1 = 1/(h->f[which].sd_cc);
t2 = (score[i]-(h->f[which].m_cc))/h->f[which].sd_cc;
t3 = fabs(t2);
t4 = pow(t3,2);
t4 = t3*t3;
Gcc = t1 * exp(-0.5*t4);
/* printf("Gcc %f %f %f %f %f\n",t1cc,t2cc,t3cc,t4cc,Gcc); */
t1 = 1/(h->f[which].sd_g);
t2 = (score[i]-(h->f[which].m_g))/h->f[which].sd_g;
t3 = fabs(t2);
t4 = pow(t3,2);
t4 = t3*t3;
Gg = t1 * exp(-0.5*t4);
/* printf("Gg %f %f %f %f %f\n",t1g,t2g,t3g,t4g,Gg); */
P[i] = Gcc/(h->f[which].sc*Gg+Gcc);
if(P[i]>=min_P) {
are_there_coils=1;
if((i==0) || (P[i-1]<min_P)) { total_coil_segments++; }
(*tc)++;
}
(*t)++;
if(mode==1) {
if(P[i]>=min_P) { printf("x"); }
else { printf("%c",seq[i]); }
if(((i+1)%60)==0) { printf("\n"); }
} else if(mode==0) {
printf("%4d %c %c %7.3f %7.3f (%7.3f %7.3f)\n",i+1,seq[i],hept_seq[i],score[i],P[i],Gcc,Gg);
}
}
if(mode==1) { printf("\n"); }
if((mode==2) && (are_there_coils==1) && (total_coil_segments>=min_seg)) {
if(total_coil_segments==1) {
printf("Pred %4d coil segment : %s %s\n",total_coil_segments,ident,title);
} else {
printf("Pred %4d coil segments : %s %s\n",total_coil_segments,ident,title);
}
}
free(P); free(score); free(hept_seq);
}
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