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Copy pathpauc_forback_anc_lib.cpp
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pauc_forback_anc_lib.cpp
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#define _CRT_SECURE_NO_WARNINGS
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <time.h>
#include <ctype.h>
#define Min(a,b) ((a)>(b))? (b):(a);
#define Max(a,b) ((a)>(b))? (a):(b);
#define SEQLEN 12000
#define MATLEN 50 // max length of motives
#define OLIGNUM 4// di 16 mono 4
#define ARGLEN 300 //max argv length
#define MAXPAR 1500 //max no. of motifs
#define NUM_LIBRARY 7// 4islo bibliotek
struct acc {
double auc1;
double auc2;
double sim;
int rank;
int num;
int best;
};
struct qbs {
double err;//ERR score
int tpr;
int fpr;
int fps;
};
int compare_qq(const void* X1, const void* X2)//increase
{
double X = (*(double*)X1 - *(double*)X2);
if (X > 0)return -1;
if (X < 0)return 1;
return 0;
}
int compare_qbs(const void* X1, const void* X2)//decrease
{
struct qbs* S1 = (struct qbs*)X1;
struct qbs* S2 = (struct qbs*)X2;
if (S1->err - S2->err > 0)return -1;
if (S1->err - S2->err < 0)return 1;
return 0;
}
int compare_auc(const void* X1, const void* X2)//decrease
{
struct acc* S1 = (struct acc*)X1;
struct acc* S2 = (struct acc*)X2;
if (S1->best - S2->best > 0)return -1;
if (S1->best - S2->best < 0)return 1;
if (S1->auc2 - S2->auc2 > 0)return -1;
if (S1->auc2 - S2->auc2 < 0)return 1;
return 0;
}
int compare_num(const void* X1, const void* X2)//decrease
{
struct acc* S1 = (struct acc*)X1;
struct acc* S2 = (struct acc*)X2;
if (S1->num - S2->num > 0)return 1;
if (S1->num - S2->num < 0)return -1;
return 0;
}
void DelHole(char* str)
{
char* hole;
hole = strstr(str, "\n");
if (hole != NULL) *hole = 0;
}
char* TransStr(char* d)
{
int i, c, lens;
lens = (int)strlen(d);
for (i = 0; i < lens; i++)
{
c = int(d[i]);
if (c < 97) d[i] = char(c + 32);
//else break;
}
return(d);
}
int CheckStr(char* file, char* d, int n, int print)
{
int i, len, ret;
len = (int)strlen(d);
ret = 1;
for (i = 0; i < len; i++)
{
int di = (int)d[i];
if (strchr("atgcATGC", di) != NULL)continue;
if (strchr("nN", di) != NULL)
{
ret = 0; continue;
}
if (print == 1)printf("File %s; sequence %d position %d (%c) bad. Sequence deleted!\n", file, n, i + 1, d[i]);
ret = -1;
break;
}
return(ret);
}
int IdeLet(char c)
{
int ret;
switch (c) {
case 'a': ret = 0; break;
case 'c': ret = 1; break;
case 'g': ret = 2; break;
case 't': ret = 3; break;
case 'n': ret = -1; break;
default: ret = -2;
}
return(ret);
}
void EvalSeq(char* file, int& nseq, int olen, int len_peak_max)
{
char l[SEQLEN], d[SEQLEN], head[400];
int fl = 0;
FILE* in;
if ((in = fopen(file, "rt")) == NULL)
{
printf("EvalSeq! Input file %s can't be opened!\n", file);
exit(1);
}
char symbol = fgetc(in);
rewind(in);
nseq = 0;
int n = 0;
while (n >= 0)
{
if (fgets(l, sizeof(l), in) == NULL) fl = -1;
if (*l == '\n' && fl != -1)continue;
if (((*l == symbol) || (fl == -1)) && (fl != 0))
{
int lenx = (int)strlen(d);
int check = CheckStr(file, d, n, 1);
if ((lenx >= olen && lenx <= len_peak_max) && check != -1)nseq++;
if (fl == -1)
{
fclose(in);
break;
}
n++;
}
if (*l == symbol)
{
memset(head, 0, sizeof(head));
DelHole(l);
strcpy(head, l);
fl = 0; continue;
}
if (fl == 0)
{
memset(d, 0, sizeof(d));
DelHole(l);
strcpy(d, l);
fl = 1; continue;
}
if (strlen(d) + strlen(l) > sizeof(d))
{
printf("Size is large...");
printf("l:%s\nstrlen(l):%zu\n", l, strlen(l));
printf("d:%s\nstrlen(d):%zu\n", d, strlen(d));
exit(1);
}
DelHole(l);
strcat(d, l);
}
}
void EvalLen(char* file, int* len, int olen, int len_peak_max)
{
char l[SEQLEN], d[SEQLEN], head[400];
int fl = 0;
FILE* in;
if ((in = fopen(file, "rt")) == NULL)
{
printf("EvalLen! Input file %s can't be opened!\n", file);
exit(1);
}
char symbol = fgetc(in);
rewind(in);
int nn = 0;
int n = 0;
while (n >= 0)
{
if (fgets(l, sizeof(l), in) == NULL) fl = -1;
if (*l == '\n' && fl != -1)continue;
if (((*l == symbol) || (fl == -1)) && (fl != 0))
{
int lenx = (int)strlen(d);
int check = CheckStr(file, d, nn, 0);
if ((lenx >= olen && lenx <= len_peak_max) && check != -1)len[n++] = lenx;
nn++;
if (fl == -1)
{
fclose(in);
break;
}
}
if (*l == symbol)
{
memset(head, 0, sizeof(head));
DelHole(l);
strcpy(head, l);
fl = 0; continue;
}
if (fl == 0)
{
memset(d, 0, sizeof(d));
DelHole(l);
strcpy(d, l);
fl = 1; continue;
}
if (strlen(d) + strlen(l) > sizeof(d))
{
printf("Size is large...");
printf("l:%s\nstrlen(l):%zu\n", l, strlen(l));
printf("d:%s\nstrlen(d):%zu\n", d, strlen(d));
exit(1);
}
DelHole(l);
strcat(d, l);
}
}
int ComplStr(char* d)
{
int i, len;
len = (int)strlen(d);
char d1[SEQLEN];
strcpy(d1, d);
// memset(d,0,sizeof(d));
for (i = 0; i < len; i++)
{
switch (d1[len - i - 1])
{
case 'a': {d[i] = 't'; break; }
case 't': {d[i] = 'a'; break; }
case 'c': {d[i] = 'g'; break; }
case 'g': {d[i] = 'c'; break; }
default: d[i] = 'n';
}
}
return 1;
}
void ReadSeq(char* file, int nseq, int* len, char*** seq_real, int olen, int len_peak_max)
{
char l[SEQLEN], d[2][SEQLEN], head[400];
int fl = 0, i, j;
FILE* in;
if ((in = fopen(file, "rt")) == NULL)
{
printf("ReadSeq! Input file %s can't be opened!\n", file);
exit(1);
}
char symbol = fgetc(in);
rewind(in);
int size = 1;
int nn = 0, n = 0;
while (n >= 0)
{
if (fgets(l, sizeof(l), in) == NULL) fl = -1;
if (*l == '\n' && fl != -1)continue;
if (((*l == symbol) || (fl == -1)) && (fl != 0))
{
int lenx = (int)strlen(d[0]);
int check = CheckStr(file, d[0], nn, 0);
nn++;
if ((lenx >= olen && lenx <= len_peak_max) && check != -1)
{
TransStr(d[0]);
d[0][len[n]] = '\0';
strcpy(d[1], d[0]);
ComplStr(d[1]);
d[1][len[n]] = '\0';
for (j = 0; j < 2; j++)
{
for (i = 0; i < lenx; i++)
{
seq_real[j][n][i] = d[j][i];
}
seq_real[j][n][lenx] = '\0';
}
n++;
}
else
{
if (lenx < olen)
{
printf("ReadSeq! Short peak %d (Len %d) ignored\n", nn + 1, lenx);
}
if (lenx > len_peak_max)
{
printf("ReadSeq! Long peak %d (Len %d) ignored\n", nn + 1, lenx);
}
if (check == -1)
{
printf("ReadSeq! Unusual symbol, peak %d ignored\n%s\n", nn + 1, d[0]);
}
}
if (fl == -1)
{
fclose(in);
break;
}
}
if (*l == symbol)
{
memset(head, 0, sizeof(head));
DelHole(l);
strcpy(head, l);
fl = 0; continue;
}
if (fl == 0)
{
memset(d[0], 0, sizeof(d[0]));
DelHole(l);
strcpy(d[0], l);
fl = 1; continue;
}
if (strlen(d[0]) + strlen(l) > sizeof(d[0]))
{
printf("Size is large...");
printf("l:%s\nstrlen(l):%zu\n", l, strlen(l));
printf("d:%s\nstrlen(d):%zu\n", d[0], strlen(d[0]));
exit(1);
}
DelHole(l);
strcat(d[0], l);
}
}
// ras4et 4asot oligonukleotidov po stroke (zdes' - nukleotidov)
void GetSostPro(char* d, int word, int* sost)
{
int i, j, k, i_sost, let;
char letter[] = "acgt";
int ten[6] = { 1, 4, 16, 64, 256, 1024 };
int lens = strlen(d);
int size = 1;
for (k = 0; k < word; k++)size *= 4;
for (i = 0; i < size; i++)sost[i] = 0;
for (i = 0; i < lens - word + 1; i++)
{
i_sost = 0;
let = -1;
for (j = word - 1; j >= 0; j--)
{
for (k = 0; k < 4; k++)
{
if (d[i + j] == letter[k]) { let = k; break; }
}
i_sost += ten[word - 1 - j] * let;
}
sost[i] = i_sost;
}
}
void PWMScore(double(&pwm)[MATLEN][OLIGNUM], double& min, double& raz, int len1)
{
int i, j;
for (i = 0; i < len1; i++)
{
double pwmmin = 100;
double pwmmax = -100;
for (j = 0; j < OLIGNUM; j++)
{
if (pwm[i][j] < pwmmin)pwmmin = pwm[i][j];
if (pwm[i][j] > pwmmax)pwmmax = pwm[i][j];
}
raz += pwmmax;
min += pwmmin;
}
raz -= min;
}
int PWM_rec_real_one(double(&pwm)[MATLEN][OLIGNUM], double min, double raz, int nthr_dist, double* thr_all, double* fpr_all, int* tpr, int olen, int nseq, char*** seq)
{
int i, j, n;
int compl1;
int cod[MATLEN];
char d[MATLEN];
int word = 1;
int nthr_dist1 = nthr_dist - 1;
double thr_cr = thr_all[nthr_dist1];
for (n = 0; n < nseq; n++)
{
//if ((n + 1) % 500 == 0)printf("\b\b\b\b\b\b\b%7d", n + 1);
int len_pro1 = strlen(seq[0][n]);
int len21 = len_pro1 - olen;
int index = nthr_dist;
for (i = 0; i <= len21; i++)
{
double sco2 = 0;
int gom = 0;
for (compl1 = 0; compl1 < 2; compl1++)
{
int ista;
if (compl1 == 0)ista = i;
else ista = len21 - i;
strncpy(d, &seq[compl1][n][ista], olen);
d[olen] = '\0';
if (strstr(d, "n") != NULL) { gom = 1; break; }
GetSostPro(d, word, cod);
double score = 0;
for (j = 0; j < olen; j++)
{
score += pwm[j][cod[j]];
}
score -= min;
score /= raz;
if (score > sco2)sco2 = score;
}
if (gom == 0)
{
if (sco2 >= thr_cr)
{
if (sco2 >= thr_all[0])
{
index = 0;
break;
}
else
{
int index_here = nthr_dist;
for (j = 1; j < nthr_dist; j++)
{
if (sco2 >= thr_all[j] && sco2 < thr_all[j - 1])
{
index_here = j;
break;
}
}
if (index_here < index)index = index_here;
}
}
if (index == 0)break;
}
}
for (j = index; j <= nthr_dist; j++)tpr[j]++;
}
return 1;
}
int PWM_rec_back_one(double(&pwm)[MATLEN][OLIGNUM], double min, double raz, int nthr_dist, double* thr_all, double* fpr_all, int* fpr, int* fp_nsites, int olen, int nseq, char*** seq, int& all_pos)
{
int i, j, n;
int compl1;
int cod[MATLEN];
char d[MATLEN];
int word = 1;
int nthr_dist1 = nthr_dist - 1;
double thr_cr = thr_all[nthr_dist1];
for (n = 0; n < nseq; n++)
{
//if ((n+1) % 500 == 0)printf("\b\b\b\b\b\b\b%7d", n+1);
int len_pro1 = strlen(seq[0][n]);
int len21 = len_pro1 - olen;
int index_best = nthr_dist;
for (i = 0; i <= len21; i++)
{
double sco2 = 0;
int gom = 0;
for (compl1 = 0; compl1 < 2; compl1++)
{
int ista;
if (compl1 == 0)ista = i;
else ista = len21 - i;
strncpy(d, &seq[compl1][n][ista], olen);
d[olen] = '\0';
if (strstr(d, "n") != NULL) { gom = 1; break; }
all_pos++;
GetSostPro(d, word, cod);
double score = 0;
for (j = 0; j < olen; j++)
{
score += pwm[j][cod[j]];
}
score -= min;
score /= raz;
if (score > sco2)sco2 = score;
}
if (gom == 0)
{
all_pos++;
int index = nthr_dist;
if (sco2 >= thr_cr)
{
if (sco2 >= thr_all[0])
{
index = 0;
}
else
{
for (j = 1; j < nthr_dist; j++)
{
if (sco2 >= thr_all[j] && sco2 < thr_all[j - 1])
{
index = j;
break;
}
}
}
}
for (j = nthr_dist; j >= index; j--)fp_nsites[j]++;
if (index < index_best)index_best = index;
}
}
for (j = index_best; j <= nthr_dist; j++)fpr[j]++;
}
return 1;
}
int PWM_rec_real(double(&pwm)[2][MATLEN][OLIGNUM], double min[2], double raz[2], int nthr_dist[2], double** thr_all, double** fpr_all, int** tp_two, int olen[2], int nseq, char*** seq)
{
int i, j, k, n;
int compl1;
int cod[MATLEN];
char d[MATLEN];
int word = 1;
int nthr_dist1[2], olen1[2];
double thr_cr[2];
for (n = 0; n < 2; n++)
{
nthr_dist1[n] = nthr_dist[n] - 1;
olen1[n] = olen[n] - 1;
thr_cr[n] = thr_all[n][nthr_dist1[n]];
}
for (n = 0; n < nseq; n++)
{
//if ((n + 1) % 500 == 0)printf("\b\b\b\b\b\b\b%7d", n + 1);
int best_inx[2];
for (k = 0; k < 2; k++)
{
int index;
int len_pro1 = strlen(seq[0][n]);
int len21 = len_pro1 - olen[k];
index = best_inx[k] = nthr_dist[k];
for (i = 0; i <= len21; i++)
{
double sco2 = 0;
int gom = 0;
for (compl1 = 0; compl1 < 2; compl1++)
{
int ista;
if (compl1 == 0)ista = i;
else ista = len21 - i;
strncpy(d, &seq[compl1][n][ista], olen[k]);
d[olen[k]] = '\0';
if (strstr(d, "n") != NULL) { gom = 1; break; }
GetSostPro(d, word, cod);
double score = 0;
for (j = 0; j < olen[k]; j++)
{
score += pwm[k][j][cod[j]];
}
score -= min[k];
score /= raz[k];
if (score > sco2)sco2 = score;
}
if (gom == 0)
{
if (sco2 >= thr_cr[k])
{
if (sco2 >= thr_all[k][0])
{
index = 0;
break;
}
else
{
for (j = 1; j < nthr_dist[k]; j++)
{
if (sco2 >= thr_all[k][j] && sco2 < thr_all[k][j - 1])
{
index = j;
break;
}
}
}
}
if (index < best_inx[k])best_inx[k] = index;
if (index == 0)break;
}
}
}
if (fpr_all[0][best_inx[0]] > fpr_all[1][best_inx[1]])tp_two[0][best_inx[0]]++;
else tp_two[1][best_inx[1]]++;
}
/*
int sum = 0;
for (i = 0; i < 2; i++)
{
for (j = 0; j < nthr_dist[i]; j++)
{
sum += tp_two[i][j];
}
}*/
return 1;
}
// position frequency mattrix (PFM), position weight matrix (PWM)
struct matrices {
int len;
double** fre;
void get_copy(matrices* a);
int mem_in(int len);
void mem_out(int len);
void norm(void);
};
int matrices::mem_in(int length)
{
int i;
len = length;
fre = new double* [len];
if (fre == NULL) return -1;
for (i = 0; i < len; i++)
{
fre[i] = new double[OLIGNUM];
if (fre[i] == NULL) return -1;
}
return 1;
}
void matrices::mem_out(int len)
{
int i;
for (i = 0; i < len; i++) delete[] fre[i];
delete[] fre;
}
void matrices::get_copy(matrices* a)
{
a->mem_in(len);
a->len = len;
int i, j;
for (i = 0; i < len; i++)
{
for (j = 0; j < OLIGNUM; j++)
{
a->fre[i][j] = fre[i][j];
}
}
}
#include "pfm_similarity.h" //permutation test for anchor/partner motif comparison (separate task for all algorithm)
#include "pfm_families.h"
#include "pfm_classes.h"
#include "pfm_list.h" //motifs
#include "pfm_tfs.h" //TFs
int main(int argc, char* argv[])
{
int i, j, k, mot1;
char*** seq_real, *** seq_back;
char file_for[ARGLEN], file_back[ARGLEN], file_log[ARGLEN], partner_db[ARGLEN], anchor[ARGLEN];// , pfile_for[ARGLEN], pfile_back[ARGLEN];// , tfclass[80];// path_fasta[ARGLEN],
char file_auc[ARGLEN];
FILE* out_log, * out_auc, * in_pwm[2];
if (argc != 8)
{
printf("%s 1,2input fasta foreground,background 3,4input model's binary files anchor,library 5double ERRthresh 6,7files out pAUC_list log", argv[0]);
return -1;
}
strcpy(file_for, argv[1]);
strcpy(file_back, argv[2]);
strcpy(anchor, argv[3]);
strcpy(partner_db, argv[4]); //h12hs, h12mm
double fp2 = atof(argv[5]); //ERR threshold for pAUC-PR
strcpy(file_auc, argv[6]);
strcpy(file_log, argv[7]);
int* len_real, * len_back, nseq_real = 0, nseq_back = 0;
int olen_min = 8;
int len_peak_max = 3000;
// double fp2 = 0.005; //FPR threshold for pAUC
double fp2_lg = -log10(fp2);
int s_overlap_min = 6, s_ncycle_small = 1000, s_ncycle_large = 10000;//for permutation(motif_comparison) min_length_of_alignment, no. of permutation (test & detailed)
double s_granul = 0.001;//for permutation(motif_comparison) okruglenie 4astotnyh matric
double p_crit = 0.05;// threshold for similarity of matrices
double pval_sim[4];
matrices matrix[2];
if ((out_auc = fopen(file_auc, "wt")) == NULL)
{
fprintf(out_auc, "Input file %s can't be opened!\n", file_auc);
exit(1);
}
if ((out_log = fopen(file_log, "wt")) == NULL)
{
fprintf(out_log, "Input file %s can't be opened!\n", file_log);
exit(1);
}
fprintf(out_log, "# Partner motif\tAnchor\tPartner TF\tPartner Motif\tAnchor pAUC\tPartner pAUC\tA&P pAUC\tRatio\tSimilarity\t\tPartner Class\tPartner Family\n");
// printf("EvalSeq\n");
EvalSeq(file_for, nseq_real, olen_min, len_peak_max);
EvalSeq(file_back, nseq_back, olen_min, len_peak_max);
len_real = new int[nseq_real];
if (len_real == NULL) { puts("Out of memory..."); exit(1); }
len_back = new int[nseq_back];
if (len_back == NULL) { puts("Out of memory..."); exit(1); }
//printf("EvalLen\n");
EvalLen(file_for, len_real, olen_min, len_peak_max);
EvalLen(file_back, len_back, olen_min, len_peak_max);
seq_real = new char** [2];
if (seq_real == NULL) { puts("Out of memory..."); exit(1); }
for (i = 0; i < 2; i++)
{
seq_real[i] = new char* [nseq_real];
if (seq_real[i] == NULL) { puts("Out of memory..."); exit(1); }
for (j = 0; j < nseq_real; j++)
{
seq_real[i][j] = new char[len_real[j] + 1];
if (seq_real[i][j] == NULL) { puts("Out of memory..."); exit(1); }
}
}
seq_back = new char** [2];
if (seq_back == NULL) { puts("Out of memory..."); exit(1); }
for (i = 0; i < 2; i++)
{
seq_back[i] = new char* [nseq_back];
if (seq_back[i] == NULL) { puts("Out of memory..."); exit(1); }
for (j = 0; j < nseq_back; j++)
{
seq_back[i][j] = new char[len_back[j] + 1];
if (seq_back[i][j] == NULL) { puts("Out of memory..."); exit(1); }
}
}
ReadSeq(file_for, nseq_real, len_real, seq_real, olen_min, len_peak_max);
ReadSeq(file_back, nseq_back, len_back, seq_back, olen_min, len_peak_max);
//motif library
char motif_name[MAXPAR][40], motif_class[MAXPAR][80], motif_family[MAXPAR][80], motif_class_inx[MAXPAR][8], motif_family_inx[MAXPAR][10], motif_tf[MAXPAR][30];
int n_motifs, motif_library = -1;
{// 0 1 2 3 4 5 6
char library_tag[NUM_LIBRARY][30] = { "h12core_hg38" , "h12core_mm10" , "h11core_hg38" , "h11core_mm10" , "dapseq", "jaspar24_at10", "jaspar24_dm6" };
int motif_count_library[NUM_LIBRARY] = { 1420,1142,391,346,510,556,151 };
for (i = 0; i < NUM_LIBRARY; i++)
{
if (strstr(partner_db, library_tag[i]) != NULL)
{
motif_library = i;
n_motifs = motif_count_library[i];
break;
}
}
if (motif_library == -1)
{
printf("Wrong motif library %s\tAllowed motif library options:\n", partner_db);
int i1 = NUM_LIBRARY - 1;
for (i = 0; i < NUM_LIBRARY; i++)
{
printf("%s", library_tag[i]);
if (i == i1)printf("\n");
else printf("\t");
}
exit(1);
}
switch (motif_library) {
case 0: {
for (i = 0; i < n_motifs; i++)
{
strcpy(motif_name[i], hs_core_12_names[i]);
strcpy(motif_class[i], h12hs_classes[i]);
strcpy(motif_family[i], h12hs_families[i]);
strcpy(motif_tf[i], h12hs_tfs[i]);
}
break;
}
case 1: {
for (i = 0; i < n_motifs; i++)
{
strcpy(motif_name[i], mm_core_12_names[i]);
strcpy(motif_class[i], h12mm_classes[i]);
strcpy(motif_family[i], h12mm_families[i]);
strcpy(motif_tf[i], h12mm_tfs[i]);
}
break;
}
case 5: {
for (i = 0; i < n_motifs; i++)
{
strcpy(motif_name[i], jaspar24_plants_names[i]);
strcpy(motif_class[i], jaspar24_plants_classes[i]);
strcpy(motif_family[i], jaspar24_plants_families[i]);
strcpy(motif_tf[i], jaspar24_plants_tfs[i]);
}
break;
}
case 6: {
for (i = 0; i < n_motifs; i++)
{
strcpy(motif_name[i], jaspar24_insects_names[i]);
strcpy(motif_class[i], jaspar24_insects_classes[i]);
strcpy(motif_family[i], jaspar24_insects_families[i]);
strcpy(motif_tf[i], jaspar24_insects_tfs[i]);
}
break;
}
default:
break;
}
}
for (i = 0; i < n_motifs; i++)
{
int sta, clen;
clen = strlen(motif_class[i]);
sta = 0;
char st = '{', en = '}';
for (j = 0; j < clen; j++)
{
if (motif_class[i][j] == st)
{
sta = j + 1;
break;
}
}
memset(motif_class_inx[i], '\0', sizeof(motif_class_inx[i]));
k = 0;
for (j = sta; motif_class[i][j] != en; j++)motif_class_inx[i][k++] = motif_class[i][j];
motif_family_inx[i][k] = '\0';
clen = strlen(motif_family[i]);
sta = 0;
for (j = 0; j < clen; j++)
{
if (motif_family[i][j] == st)
{
sta = j + 1;
break;
}
}
if (motif_library <= 1 || motif_library == 6)
{
memset(motif_family_inx[i], '\0', sizeof(motif_family_inx[i]));
k = 0;
for (j = sta; motif_family[i][j] != en; j++)motif_family_inx[i][k++] = motif_family[i][j];
motif_family_inx[i][k] = '\0';
}
else
{
memset(motif_family_inx[i], '\0', sizeof(motif_family_inx[i]));
}
}
if ((in_pwm[0] = fopen(anchor, "rb")) == NULL)
{
printf("Input file %s can't be opened!\n", anchor);
return -1;
}
if ((in_pwm[1] = fopen(partner_db, "rb")) == NULL)
{
printf("Input file %s can't be opened!\n", partner_db);
return -1;
}
int len_partner[2], nthr_dist[2];
double pwm[2][MATLEN][OLIGNUM];
double pfm[2][MATLEN][OLIGNUM];
int nthr_dist_max = 20000;
double** thr_all;
thr_all = new double* [2];
if (thr_all == NULL) { puts("Out of memory..."); exit(1); }
for (i = 0; i < 2; i++)
{
thr_all[i] = new double[nthr_dist_max];
if (thr_all[i] == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
}
double** fpr_all;
fpr_all = new double* [2];
if (fpr_all == NULL) { puts("Out of memory..."); exit(1); }
for (i = 0; i < 2; i++)
{
fpr_all[i] = new double[nthr_dist_max];
if (fpr_all[i] == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
}
//n_motifs = 50;
int* tp_one, * fp_one;
tp_one = new int[nthr_dist_max];
if (tp_one == NULL) { puts("Out of memory..."); exit(1); }
fp_one = new int[nthr_dist_max];
if (fp_one == NULL) { puts("Out of memory..."); exit(1); }
double* tp_here;
tp_here = new double[nthr_dist_max];
if (tp_here == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
double* fp_here;
fp_here = new double[nthr_dist_max];
if (fp_here == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
int** tp_two;
tp_two = new int* [2];
if (tp_two == NULL) { puts("Out of memory..."); exit(1); }
for (i = 0; i < 2; i++)
{
tp_two[i] = new int[nthr_dist_max];
if (tp_two[i] == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
}
int** fp_two;
fp_two = new int* [2];
if (fp_two == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
for (i = 0; i < 2; i++)
{
fp_two[i] = new int[nthr_dist_max];
if (fp_two[i] == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
}
int** fp_nsites;// frequencies
fp_nsites = new int* [2];
if (fp_nsites == NULL) { puts("Out of memory..."); exit(1); }
for (i = 0; i < 2; i++)
{
fp_nsites[i] = new int[nthr_dist_max];
if (fp_nsites[i] == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
}
qbs* tab;
tab = new qbs[2 * nthr_dist_max];
if (tab == NULL) { puts("Out of memory..."); exit(1); }
int nmot_max = 1500;
acc* motifp;
motifp = new acc[n_motifs];
if (motifp == NULL) { fprintf(stderr, "Error: Out of memory..."); return -1; }
double nseq_fb = (double)nseq_real / nseq_back;
double prec_exp = 0.5;
double min[2], raz[2];
{
fread(&len_partner[0], sizeof(int), 1, in_pwm[0]);
int len40 = 4 * len_partner[0];
fread(pfm[0], sizeof(double), len40, in_pwm[0]);
fread(pwm[0], sizeof(double), len40, in_pwm[0]);
int nthr_dist_all;
fread(&nthr_dist_all, sizeof(int), 1, in_pwm[0]);
fread(thr_all[0], sizeof(double), nthr_dist_all, in_pwm[0]);
fread(fpr_all[0], sizeof(double), nthr_dist_all, in_pwm[0]);
nthr_dist[0] = 0;
for (i = 0; i < nthr_dist_all; i++)
{
nthr_dist[0]++;
if (fpr_all[0][i] < fp2_lg)break;
}
min[0] = raz[0] = 0;
PWMScore(pwm[0], min[0], raz[0], len_partner[0]);
matrix[0].mem_in(len_partner[0]);
for (i = 0; i < len_partner[0]; i++)for (j = 0; j < OLIGNUM; j++)matrix[0].fre[i][j] = pfm[0][i][j];
}
fclose(in_pwm[0]);
int all_pos[2], all_pos_thr[2], index_thr[2];
double fp_thr_rest[2];
double auc_one[2];
{
for (j = 0; j <= nthr_dist[0]; j++)tp_one[j] = fp_one[j] = fp_nsites[0][j] = 0;
all_pos[0] = 0;
//printf("Real %d\n",mot + 1);
int pwm_check = PWM_rec_real_one(pwm[0], min[0], raz[0], nthr_dist[0], thr_all[0], fpr_all[0], tp_one, len_partner[0], nseq_real, seq_real);
if (pwm_check == -1)
{
printf("Motif %s recognition error, real\n",anchor);
exit(1);
}
//printf("Back %d\n", mot + 1);
pwm_check = PWM_rec_back_one(pwm[0], min[0], raz[0], nthr_dist[0], thr_all[0], fpr_all[0], fp_one, fp_nsites[0], len_partner[0], nseq_back, seq_back, all_pos[0]);
if (pwm_check == -1)
{
printf("Motif %s recognition error, back\n", anchor);
exit(1);
}
/*for (i = 0; i <= nthr_dist[0]; i++)
{
if ((i + 1) % 10 == 0)printf("%d\n", i + 1);
printf("%5d %d\t", tp_one[i], fp_one[i]);
}*/
//printf("ROC %d\n", mot + 1);
all_pos_thr[0] = (int)(all_pos[0] * fp2);
index_thr[0] = nthr_dist[0] - 1;
int count_one = 0;
fp_thr_rest[0]= 0;
for (i = 0; i < nthr_dist[0]; i++)
{
count_one = fp_nsites[0][i];
//printf("ERR %f Count %d FPsites %d FPpeak %d TPpeak %d\n", fpr_all[0][i], count_one, fp_nsites[0][i], fp_one[i], tp_one[i]);
if (count_one >= all_pos_thr[0])
{
index_thr[0] = i;
fp_thr_rest[0] = 1 - (double)(count_one - all_pos_thr[0]) / fp_nsites[0][i];
break;
}
}
auc_one[0] = 0;
double prec_pred = 1;// (double)tp_one[0] / ((double)tp_one[0] + nseq_fb * fp_one[0]);
// recall_1[n][0] = 0;//(double)tp_one[0]/nseq_real,
// prec_1[n][0] = prec_pred;
int n_here = 1;
int index_thr01 = index_thr[0] - 1;
for (i = 0; i <= index_thr[0]; i++)
{
int dtp = tp_one[i];
int i1 = i - 1;
if (i > 0)dtp -= tp_one[i1];
if (dtp > 0)
{
double dtpi = (double)tp_one[i];
double dfpi = (double)fp_one[i];
if (i > 0)
{
dfpi -= fp_one[i1];
dtpi -= tp_one[i1];
}
if (i == index_thr[0])
{
dtpi *= fp_thr_rest[0];
dfpi *= fp_thr_rest[0];
}