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# File 'ext/protk/protk.c', line 28
static VALUE protk_make_decoys(VALUE self,VALUE input_file_in,VALUE db_length_in,VALUE output_file_in,char *prefix_string_in) {
char *input_file = RSTRING_PTR(input_file_in);
long sequences_to_generate = NUM2INT(db_length_in);
char * output_file = RSTRING_PTR(output_file_in);
char line[MAX_LINE_LENGTH];
char settings_line[60][70];
char infile[255], outfile[255]; /* for reading input and writing output */
char prefix_string[255];
char *p,**index;
char *sequence;
char one_sequence[MAX_SEQUENCE_LENGTH],random_sequence[(int)(MAX_SEQUENCE_LENGTH*1.5)],random_sequence_output[(int)(MAX_SEQUENCE_LENGTH*1.5)];
char *temp_sequence;
int a;
FILE *inp, *outp;
long i, j, k, l, n, n_sequences, protein;
long MP[21][MAX_SEQUENCE_LENGTH];
long measured_aa_freq[21], generated_aa_freq[21], measured_pl_sum=0, generated_pl_sum=0;
long row_sum[MAX_SEQUENCE_LENGTH],partial_sum;
long one_index,pl;
double x;
/* scanning sequence database */
strcpy(infile,input_file);
if ((inp = fopen(infile, "r"))==NULL) {printf("error opening sequence database %s\n",infile);return -1;}
printf("scanning sequence database %s",infile);fflush(stdout);
i=0;n=0;k=0;
while (fgets(line, MAX_LINE_LENGTH, inp) != NULL) {i++; if(line[0]=='>') {if (!(n%1000)) printf(".");fflush(stdout); n++;} }
n_sequences=n;
/* reading sequence database */
temp_sequence=(char*)calloc(sizeof(char),MAX_SEQUENCE_LENGTH);
sequence=(char*)malloc(sizeof(char)*(i*80)); /* allocate enough memory for 80 characters per line in FASTA database */
index=(char**)malloc(sizeof(char*)*n_sequences);
index[0]=sequence; /* set first index pointer to beginning of first database sequence */
if ((inp = fopen(infile, "r"))==NULL) {printf("error opening sequence database %s\n",infile);return -1;}
printf("done\nreading sequence database %s",infile);fflush(stdout);
n=-1;
strcpy(temp_sequence,"\0");
while (fgets(line, MAX_LINE_LENGTH, inp) != NULL)
{
if (strcmp(line,"\n")==0) {
continue;
}
if (line[0]=='>') {
if (n>=0) {
if (!(n%1000)&&n>0) {
printf(".");fflush(stdout);
}
strcpy(index[n],temp_sequence);
n++; index[n]=index[n-1]+sizeof(char)*strlen(temp_sequence);
strcpy(temp_sequence,"\0");
}
else
{
n++;
strcpy(temp_sequence,"\0");
}
}
else
{
if ( (strlen(temp_sequence)+strlen(line))>=MAX_SEQUENCE_LENGTH ) continue;
strncat(temp_sequence,line,strlen(line)-1);
}
}
strcpy(index[n],temp_sequence);
fclose(inp);
n_sequences=n+1;
printf("done [read %li sequences (%li amino acids)]\n",n_sequences,(int)(index[n_sequences-1]-index[0])/sizeof(char)+strlen(temp_sequence));fflush(stdout);
measured_pl_sum=(int)(index[n_sequences-1]-index[0])/sizeof(char)+strlen(temp_sequence);
/* generating Markov probabilities */
printf("generating Markov probability matrix...");fflush(stdout);
srand(time(0)); /* replace with constant to re-generate identical random databases */
for(i=0;i<MAX_SEQUENCE_LENGTH;i++) {
for(j=0;j<=20;j++) {
MP[j][i]=0;
}
}
for(j=0;j<=20;j++) {
measured_aa_freq[j]=0;generated_aa_freq[j]=0;
}
for(protein=0;protein<n_sequences;protein++)
{
if (!(protein%1000)) {printf(".");fflush(stdout);}
if (protein<(n_sequences-1))
{
strncpy(one_sequence,index[protein],(index[protein+1]-index[protein])/sizeof(char));
one_sequence[(index[protein+1]-index[protein])/sizeof(char)]='\0';
}
else strcpy(one_sequence,index[protein]);
pl=strlen(one_sequence);
n=1;one_index=0;
for(i=0;i<pl;i++)
{
if(strpbrk(NOT_AMINO_ACIDS,(const char *)&one_sequence)==NULL)
{
if ( strchr(AMINO_ACIDS,one_sequence[i])==NULL)
{
printf("Unknown amino acid %c",one_sequence[i]);
} else {
a=20-strlen(strchr(AMINO_ACIDS,one_sequence[i])); // current amino acid
MP[a][i]++;
measured_aa_freq[a]++;
}
}
else {a=floor(20*(float)rand()/RAND_MAX);MP[a][i]++; measured_aa_freq[a]++;} // replace B, X, Z etc. with random amino acid to preserve size distribution
}
MP[20][pl]++;
measured_aa_freq[20]++; // MP[20][n] is the number of sequences of length n in the database
}
printf("done\n"); fflush(stdout);
for(i=0;i<MAX_SEQUENCE_LENGTH;i++) row_sum[i]=0;
for(i=0;i<MAX_SEQUENCE_LENGTH;i++) for(j=0;j<=20;j++) row_sum[i]+=MP[j][i];
/* generate random protein sequences through Markov chain */
strcpy(outfile,output_file);
if ((outp = fopen(outfile, "w"))==NULL) {printf("error opening output file %s\n",outfile); return -1;}
printf("generating %li random protein sequences",sequences_to_generate);fflush(stdout);
strcpy(prefix_string,RSTRING_PTR(prefix_string_in));
for(protein=0;protein<sequences_to_generate;protein++)
{
if (!(protein%1000)) {printf(".");fflush(stdout);}
i=0; j=0;
while (1)
{
x=(double)row_sum[j]*((double)rand()/RAND_MAX);
partial_sum=MP[0][j]; i=1;
while (partial_sum<x) {partial_sum+=MP[i][j]; i++;}
if (j>=MAX_SEQUENCE_LENGTH) i=21; /* terminate when sequence has reached MAX_SEQUENCE_LENGTH */
if (i<21)
{
random_sequence[j]=AMINO_ACIDS[i-1];j++;generated_aa_freq[i-1]++;
}
else /* i==21, i.e. protein sequence terminated */
{
k=0; generated_aa_freq[20]++; generated_pl_sum+=j;
for(l=0;l<j;l++)
{
random_sequence_output[k]=random_sequence[l]; k++;
if (!((k+1)%61))
{
random_sequence_output[k]='\n'; k++;
}
}
random_sequence_output[k]='\0';
if (!(k%61)) random_sequence_output[k-1]='\0'; /* remove extra newline for sequence length multiple of 60 */
fprintf(outp,">%srp%li\n%s\n",prefix_string,protein,random_sequence_output);
break;
}
}
}
fclose(outp);
/* freeing some memory... */
free(index);
printf("done (wrote %li random protein sequences to %s)\n",sequences_to_generate,outfile);
k=0;l=0;
for(i=0;i<=20;i++) {k+=measured_aa_freq[i];l+=generated_aa_freq[i];}
printf("<f(aa) in %s> <f(aa) in %s>\n",infile,outfile);
for(i=0;i<=20;i++) printf("%f %f\n",(float)measured_aa_freq[i]/k,(float)generated_aa_freq[i]/l);
printf("<average sequence length in %s> = %f\n<average sequence length in %s> = %f\n",infile,measured_pl_sum/(float)n_sequences,outfile,generated_pl_sum/(float)sequences_to_generate);
return 0;
}
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