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/* routines for finding open reading frames
*/
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include "dna_utils.h"
#include "array_arith.h"
#include "genetic_code.h"
#include "text_output.h"
#include "misc.h"
/* PUT ME IN array_arith */
int minimum_element ( int list[], int num_elements ) {
/* return element number of first element in list that contains
* the lists lowest value
*/
int i, min;
for ( i=1,min=list[0];i<num_elements;i++) {
min = MIN((list[i]),min);
}
for ( i=0;i<num_elements;i++) {
if ( min == list[i] ) return i;
}
return 0;
}
/* PUT ME in genetic_code */
int write_seq_lines ( FILE *fp, char *seq, int seq_len ) {
#define LINELENGTH 60
/* writes seq to fp, 60 characters per line */
int i;
for(i=0;i<seq_len;i++) {
if ( i && (i%LINELENGTH==0)) if ( fprintf(fp,"\n") < 0 ) return 1;
if ( fprintf(fp,"%c",seq[i]) < 0 ) return 1;
}
if ( fprintf(fp,"\n") < 0 ) return 1;
return 0;
}
int write_screen_seq_lines (char *seq, int seq_len) {
#define LINELENGTH 60
/* writes seq to text output window, 60 characters per line */
int i;
for(i=0;i<seq_len;i++) {
if ( i && (i%LINELENGTH==0)) vmessage("\n");
vmessage("%c",seq[i]);
}
vmessage("\n");
return 0;
}
char *orf_protein_seqf ( char *dna, int num_bases ) {
/* return a string containing the translation up to the next
* stop codon or end of data.
*/
char *s;
int i,j;
if ( ( NULL == ( s = ( char* ) malloc ( sizeof (char) * (num_bases))))) return NULL;
for ( i=0,j=0; i+2<num_bases; i+=3,j++ ) {
if ( ( '*' == (s[j] = codon_to_acid1(&dna[i])))) {
j++;
break;
}
}
if ( j > 0 && '*' != s[j-1] ) { /* always return * as last symbol */
s[j++] = '*';
}
s[j++] = '\0';
/* Shrink memory usage (if realloc will allow it) */
if ( ( NULL == ( s = ( char* ) realloc ( s, sizeof (char) * (j+1)))))
return NULL;
return s;
}
int write_open_frames_f ( FILE *fp, char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* finds open reading frames of length >= min_open and writes them
* to fp in fasta format
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seqf (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
sprintf(line, ">%d", starts[frame]+1);
line[strlen(line)] = ' ';
sprintf(&line[21], "%d..%d", starts[frame]+1, starts[frame]+len_open*3-3);
if ( fprintf( fp,"%s\n",line) < 0 ) goto bail_out;
if (write_seq_lines ( fp, protein, len_open )) goto bail_out;
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return 0;
bail_out:
free ( protein );
return 1;
}
int write_screen_open_frames_f ( char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* finds open reading frames of length >= min_open and writes them
* to fp in fasta format
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seqf (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
sprintf(line, ">%d", starts[frame]+1);
line[strlen(line)] = ' ';
sprintf(&line[21], "%d..%d", starts[frame]+1, starts[frame]+len_open*3-3);
vmessage("%s\n", line);
if (write_screen_seq_lines ( protein, len_open )) goto bail_out;
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return 0;
bail_out:
free ( protein );
return 1;
}
void write_open_frames_f_ft ( FILE *fp, char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* find open reading frames (plus strand) and write them to fp in
* embl ft format.
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seqf (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
strcpy( line, "FT CDS");
line[8] = ' ';
sprintf(&line[21], "%d..%d", starts[frame]+1, starts[frame]+len_open*3-3);
if ( fprintf(fp, "%s\n",line) < 0 ) goto bail_out;
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return;
bail_out:
free ( protein );
}
void write_screen_open_frames_f_ft (char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* find open reading frames (plus strand) and write them to output window
* in embl ft format.
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seqf (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
strcpy( line, "FT CDS");
line[8] = ' ';
sprintf(&line[21], "%d..%d", starts[frame]+1, starts[frame]+len_open*3-3);
vmessage("%s\n", line);
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return;
}
char *orf_protein_seq_r ( char *dna, int num_bases ) {
/* return a string containing the translation up to the next
* stop codon or end of data.
*/
char *s;
int i,j;
if ( ( NULL == ( s = ( char* ) malloc ( sizeof (char) * (num_bases))))) return NULL;
for ( i=0,j=0; i+2<num_bases; i+=3,j++ ) {
if ( ( '*' == (s[j] = codon_to_cacid1(&dna[i])))) {
j++;
break;
}
}
if ( j > 0 && '*' != s[j-1] ) { /* always return * as last symbol */
s[j++] = '*';
}
reverse_dna ( s, j-1 );
s[j++] = '\0';
if ( ( NULL == ( s = ( char* ) realloc ( s, sizeof (char) * (j+1)))))
return NULL;
return s;
}
int write_open_frames_r ( FILE *fp, char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* finds open reading frames of length >= min_open and writes them
* to fp in fasta format (minus strand)
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seq_r (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
sprintf(line, ">%d", starts[frame]+1);
line[strlen(line)] = ' ';
sprintf(&line[21], "complement(%d..%d)", starts[frame]+1, starts[frame]+len_open*3-3);
if ( fprintf(fp, "%s\n",line) < 0 ) goto bail_out;
if (write_seq_lines ( fp, protein, len_open )) goto bail_out;
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return 0;
bail_out:
free ( protein );
return 1;
}
int write_screen_open_frames_r ( char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* finds open reading frames of length >= min_open and writes them
* to text output window in fasta format (minus strand)
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seq_r (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
sprintf(line, ">%d", starts[frame]+1);
line[strlen(line)] = ' ';
sprintf(&line[21], "complement(%d..%d)", starts[frame]+1, starts[frame]+len_open*3-3);
vmessage("%s\n",line);
if (write_screen_seq_lines (protein, len_open )) goto bail_out;
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return 0;
bail_out:
free ( protein );
return 1;
}
void write_open_frames_r_ft ( FILE *fp, char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* find open reading frames (minus strand) and write them to fp in
* embl ft format.
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seq_r (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
strcpy( line, "FT CDS");
line[8] = ' ';
sprintf(&line[21], "complement(%d..%d)", starts[frame]+1, starts[frame]+len_open*3-3);
if ( fprintf(fp,"%s\n",line) < 0 ) goto bail_out;
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return;
bail_out:
free ( protein );
}
void write_screen_open_frames_r_ft (char *dna, int num_bases,
int user_start,
int user_end,
int min_open ) {
/* find open reading frames (minus strand) and write them to text output
* window in embl ft format.
*/
int starts[3], frame, len_open;
char *protein, line[80];
/* min_open -= 1; */
starts[0] = user_start-1;
starts[1] = user_start;
starts[2] = user_start+1;
frame = 0;
while ( starts[frame] < user_end - 3 * min_open ) {
if ( min_open < (len_open = strlen ( protein = (orf_protein_seq_r (
&dna[starts[frame]], user_end-starts[frame] ))))) {
memset(line,' ',80);
strcpy( line, "FT CDS");
line[8] = ' ';
sprintf(&line[21], "complement(%d..%d)", starts[frame]+1, starts[frame]+len_open*3-3);
vmessage("%s\n",line);
}
starts[frame] += 3 * (len_open) ;
frame = minimum_element(starts,3);
free ( protein );
}
return;
}
#ifdef REMOVE
main () {
/* 1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456*/
char *dna="atcgcttaaacgatgttatagacagataacagatacagatagacagatacagtaaa";
char *protein;
int len_open, min_len_open;
int i, num_bases;
int lreg,rreg;
set_dna_lookup();
init_genetic_code ();
printf("%s\n",dna);
num_bases = strlen ( dna );
printf("num_bases %d\n",num_bases);
lreg = 1;
rreg = num_bases;
min_len_open = 6;
write_open_frames_f_ft ( stdout, dna, num_bases, lreg, rreg, min_len_open );
write_open_frames_r_ft ( stdout, dna, num_bases, lreg, rreg, min_len_open );
write_open_frames_f ( stdout, dna, num_bases, lreg, rreg, min_len_open );
write_open_frames_r ( stdout, dna, num_bases, lreg, rreg, min_len_open );
}
#endif
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