static void
print_rest(FILE *f, const p3_global_settings *pa,
const seq_args *sa,
const pair_array_t *best_pairs)
{
int i;
int print_lib_sim = lib_sim_specified(pa);
fprintf(f, "ADDITIONAL OLIGOS\n");
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = 1; i < best_pairs->num_pairs; i++) {
fprintf(f, "\n%2d ", i);
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, best_pairs->pairs[i].left, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, best_pairs->pairs[i].left, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
fprintf(f, " ");
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, best_pairs->pairs[i].right, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, best_pairs->pairs[i].right, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
if(pa->pick_internal_oligo==1) {
fprintf(f, " ");
if(pa->modify_internal_oligo==1) {
/* Modified internal oligo */
/* printing internal_oligo_direction - 20121204 N.Kasahara */
if((best_pairs->pairs[i].intl)->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW,sa, best_pairs->pairs[i].intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
} else if((best_pairs->pairs[i].intl)->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV,sa, best_pairs->pairs[i].intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
}
} else {
/* Normal internal oligo */
/* printing internal_oligo_direction - 20121204 N.Kasahara */
if((best_pairs->pairs[i].intl)->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, best_pairs->pairs[i].intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
} else if((best_pairs->pairs[i].intl)->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, best_pairs->pairs[i].intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
}
}
}
if (best_pairs->pairs[i].product_size > 0) {
fprintf(f, " ");
print_pair_info(f, &best_pairs->pairs[i], pa);
/* Print penalty score - Y.Kimura */
fprintf(f, " ");
fprintf(f, "penalty score: %.4f\n", best_pairs->pairs[i].pair_quality);
}
}
}
static void
format_pairs(FILE *f,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
const pair_array_t *best_pairs,
const char *pr_release,
const pr_append_str *combined_retval_err,
int explain_flag)
{
char *warning;
int print_lib_sim = lib_sim_specified(pa);
primer_rec *h = NULL;
PR_ASSERT(NULL != f);
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
/* If there are errors, print them and return */
if (!pr_is_empty(combined_retval_err)) {
format_error(f, sa->sequence_name,
pr_append_str_chars(combined_retval_err));
return;
}
/* Print the sequence name if it is provided */
if (NULL != sa->sequence_name)
fprintf(f, "PRIMER PICKING RESULTS FOR %s\n\n", sa->sequence_name);
/* Print if a mispriming libraby was used and which one */
if (pa->p_args.repeat_lib != NULL)
fprintf(f, "Using mispriming library %s\n",
pa->p_args.repeat_lib->repeat_file);
else
fprintf(f, "No mispriming library specified\n");
/* Print if a mispriming libraby for the internal oligo
* was used and which one */
if ( pa->pick_internal_oligo == 1 ) {
if (pa->o_args.repeat_lib != NULL)
fprintf(f, "Using internal oligo mishyb library %s\n",
pa->o_args.repeat_lib->repeat_file);
else
fprintf(f, "No internal oligo mishyb library specified\n");
}
/* Does the sequence start at position 0 or 1 ? */
fprintf(f, "Using %d-based sequence positions\n",
pa->first_base_index);
/* Complain if no primers are in the array */
if (best_pairs->num_pairs == 0) fprintf(f, "NO PRIMERS FOUND\n\n");
/* Print out the warings */
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
fprintf(f, "WARNING: %s\n\n", warning);
free(warning);
}
/* Print the results for the best pair */
print_summary(f, pa, sa, best_pairs, 0);
fprintf(f, "\n");
/* Print nicely out the sequence with the best pair */
if (print_seq(f, pa, sa, retval, h, best_pairs, 0)) exit(-2); /* ENOMEM */
/* Print out the alternative pairs */
if (best_pairs->num_pairs > 1 ) print_rest(f, pa, sa, best_pairs);
/* Print the primer picking statistics */
if (explain_flag)
print_explain(f, pa, sa, retval, print_lib_sim, pr_release);
/* Flush the buffers and return */
fprintf(f, "\n\n");
if (fflush(f) == EOF) {
perror("fflush(f) failed");
exit(-1);
}
}
/* add branching condition for printing internal_oligo_direction and modification
* Created - 20121204 N.Kasahara
* Modified - 20140109 Y.Kimura
*/
static void
print_summary(FILE *f, const p3_global_settings *pa,
const seq_args *sa, const pair_array_t *best_pairs,
int num)
{
int seq_len = strlen(sa->sequence);
int print_lib_sim = lib_sim_specified(pa);
primer_pair *p;
p = best_pairs->pairs + num;
if (best_pairs->num_pairs > 0) {
/*
* If the following format changes, also change the format in print_oligo.
*/
print_oligo_header(f, "\nOLIGO ", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, p->left, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, p->left, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, p->right, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, p->right, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
if ( pa->pick_internal_oligo == 1 ) {
if(pa->modify_internal_oligo==1) {
/* Modified internal probe */
if((p->intl)->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, p->intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
} else if((p->intl)->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, p->intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
}
} else {
/* Internal probe */
if((p->intl)->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, p->intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
} else if((p->intl)->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, p->intl, OT_INTL, pa, pa->o_args.repeat_lib, print_lib_sim);
}
}
}
}
if (best_pairs->num_pairs > 0) {
print_pair_info(f, p, pa);
/* Print penalty score - Y.Kimura */
fprintf(f, "penalty score: %.4f\n", p->pair_quality);
}
fprintf(f, "\n");
fprintf(f, "SEQUENCE SIZE: %d\n", seq_len);
fprintf(f, "INCLUDED REGION SIZE: %d\n", sa->incl_l);
if(sa->tar2.genotyping==0) {
print_pair_array(f, "TARGETS", sa->tar2.count, sa->tar2.pairs, pa, sa);
} else if(sa->tar2.genotyping==1) {
fprintf(f,"TARGET VARIANT * (position,size):");
if(sa->tar2.char_count==sa->tar2.VAR_sequence_number) {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]-1);
} else {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]);
}
fprintf(f,"\n\n");
}
print_pair_array(f, "EXCLUDED REGIONS", sa->excl2.count, sa->excl2.pairs, pa, sa);
print_pair_array(f, "INTERNAL PROBE EXCLUDED REGIONS", sa->excl_internal2.count, sa->excl_internal2.pairs, pa, sa);
print_2_pair_array(f, "PAIR_OK_REGIONS", sa->ok_regions.count, sa->ok_regions.left_pairs, sa->ok_regions.right_pairs, pa, sa);
}
static void
format_oligos(FILE *f,
const p3_global_settings *pa,
const seq_args *sa,
const p3retval *retval,
const char* pr_release,
const pr_append_str *combined_retval_err,
int explain_flag)
{
char *warning;
int print_lib_sim = lib_sim_specified(pa);
int i;
int print_primers = 0;
primer_rec *h = NULL;
pair_array_t *best_pairs;
primer_rec *p;
int rest_count = 0;
PR_ASSERT(NULL != f);
PR_ASSERT(NULL != pa);
PR_ASSERT(NULL != sa);
best_pairs = NULL;
if (!pr_is_empty(combined_retval_err)) {
format_error(f, sa->sequence_name, pr_append_str_chars(combined_retval_err));
return;
}
if (NULL != sa->sequence_name)
fprintf(f, "PRIMER PICKING RESULTS FOR %s\n\n", sa->sequence_name);
if (pa->pick_left_primer || pa->pick_right_primer) {
if (pa->p_args.repeat_lib != NULL)
fprintf(f, "Using mispriming library %s\n",
pa->p_args.repeat_lib->repeat_file);
else
fprintf(f, "No mispriming library specified\n");
}
if (pa->pick_internal_oligo) {
if (pa->o_args.repeat_lib != NULL)
fprintf(f, "Using internal probe mishyb library %s\n", pa->o_args.repeat_lib->repeat_file);
else
fprintf(f, "No internal probe mishyb library specified\n");
}
fprintf(f, "Using %d-based sequence positions\n", pa->first_base_index);
if (pa->pick_left_primer) {
if (retval->fwd.num_elem == 0) {
fprintf(f, "NO LEFT PRIMER FOUND\n\n");
} else {
print_primers = 1;
}
}
if (pa->pick_internal_oligo) {
if (retval->intl.num_elem == 0) {
fprintf(f, "NO INTERNAL PROBE FOUND\n\n");
} else {
print_primers = 1;
}
}
if (pa->pick_right_primer) {
if (retval->rev.num_elem == 0) {
fprintf(f, "NO RIGHT PRIMER FOUND\n\n");
} else {
print_primers = 1;
}
}
if ((warning = p3_get_rv_and_gs_warnings(retval, pa)) != NULL) {
fprintf(f, "\nWARNING: %s\n", warning);
free(warning);
}
if ((pa->primer_task != pick_primer_list ) && (pa->primer_task != pick_sequencing_primers)) {
if (print_primers == 1) {
print_oligo_header(f, "OLIGO", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
}
/* Print out the first line with the best primers */
if ((pa->pick_left_primer) && (&retval->fwd != NULL ) && (retval->fwd.num_elem > 0)) {
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, retval->fwd.oligo, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, retval->fwd.oligo, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
h = retval->fwd.oligo;
rest_count = 1;
}
if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) && (retval->intl.num_elem > 0)) {
if(pa->modify_internal_oligo==1) {
if((retval->intl.oligo)->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if((retval->intl.oligo)->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
} else {
if((retval->intl.oligo)->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if((retval->intl.oligo)->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, retval->intl.oligo, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
h = retval->intl.oligo;
rest_count = 1;
}
if ((pa->pick_right_primer) && (&retval->rev != NULL ) && (retval->rev.num_elem > 0)) {
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, retval->rev.oligo, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, retval->rev.oligo, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
h = retval->rev.oligo;
rest_count = 1;
}
}
if(print_primers == 1) {
fprintf(f, "SEQUENCE SIZE: %ld\n", (long int) strlen(sa->sequence));
fprintf(f, "INCLUDED REGION SIZE: %d\n\n", sa->incl_l);
if(sa->tar2.genotyping==0) {
print_pair_array(f, "TARGETS", sa->tar2.count, sa->tar2.pairs, pa, sa);
} else if(sa->tar2.genotyping==1) {
fprintf(f,"TARGET VARIANT * (position,size):");
if(sa->tar2.char_count==sa->tar2.VAR_sequence_number) {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]-1);
} else {
fprintf(f," %d,%d",sa->tar2.VAR_start[0],sa->tar2.char_num[sa->tar2.VAR_sequence_number]);
}
fprintf(f,"\n\n");
}
print_pair_array(f, "EXCLUDED REGIONS", sa->excl2.count, sa->excl2.pairs, pa, sa);
print_pair_array(f, "INTERNAL PROBE EXCLUDED REGIONS", sa->excl_internal2.count, sa->excl_internal2.pairs, pa, sa);
print_2_pair_array(f, "PAIR_OK_REGIONS", sa->ok_regions.count, sa->ok_regions.left_pairs, sa->ok_regions.right_pairs, pa, sa);
}
if (pa->primer_task != pick_primer_list ) {
if(pa->pick_internal_oligo==1) {
if(print_seq(f,pa,sa,retval,retval->intl.oligo,best_pairs,0)) exit(-2);
}
else if(pa->pick_left_primer==1) {
if(print_seq(f,pa,sa,retval,retval->fwd.oligo,best_pairs,0)) exit(-2);
}
else if(pa->pick_right_primer==1) {
if(print_seq(f,pa,sa,retval,retval->rev.oligo,best_pairs,0)) exit(-2);
}
else if (print_seq(f, pa, sa, retval, h, best_pairs, 0)) exit(-2); /* ENOMEM */
}
fprintf(f, "\n");
/* Print out the other primers */
if ((pa->pick_left_primer) && (&retval->fwd != NULL ) && (retval->fwd.num_elem > rest_count)) {
int n = retval->fwd.num_elem;
h = retval->fwd.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_left_primer==1) {
print_oligo_Z(f, TITLE_MOD_LEFT, sa, p, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_LEFT, sa, p, OT_LEFT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
if (rest_count == 0) {
fprintf(f, "\n ");
}
}
if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) && (retval->intl.num_elem > rest_count)) {
int n = retval->intl.num_elem;
h = retval->intl.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_internal_oligo==1) {
if(p->oligo_dir==0) {
print_oligo_Z(f, TITLE_MOD_INTL_FW, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if(p->oligo_dir==1) {
print_oligo_Z(f, TITLE_MOD_INTL_RV, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
} else {
if(p->oligo_dir==0) {
print_oligo_Z(f, TITLE_INTL_FW, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
} else if(p->oligo_dir==1) {
print_oligo_Z(f, TITLE_INTL_RV, sa, p, OT_INTL, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
}
if (rest_count == 0) {
fprintf(f, "\n ");
}
}
if ((pa->pick_right_primer) && (&retval->rev != NULL ) && (retval->rev.num_elem > rest_count)) {
int n = retval->rev.num_elem;
h = retval->rev.oligo;
if (rest_count == 1) {
fprintf(f, "ADDITIONAL OLIGOS\n");
}
fprintf(f, " ");
print_oligo_header(f, "", print_lib_sim, pa->thermodynamic_alignment, sa->tar2.genotyping);
for (i = rest_count; i < pa->num_return; i++) {
if(i > n-1) break;
p = h + i;
fprintf(f, "%2d ", i + 1 - rest_count);
if(pa->modify_right_primer==1) {
print_oligo_Z(f, TITLE_MOD_RIGHT, sa, p, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
} else {
print_oligo_Z(f, TITLE_RIGHT, sa, p, OT_RIGHT, pa, pa->p_args.repeat_lib, print_lib_sim);
}
}
}
if (explain_flag)
print_explain(f, pa, sa, retval, print_lib_sim, pr_release);
fprintf(f, "\n\n");
if (fflush(f) == EOF) {
perror("fflush(f) failed");
exit(-1);
}
}
