/* See comments in p3_seq_lib.h */
seq_lib *
read_and_create_seq_lib(const char * filename, const char *errfrag) {
char *p;
FILE *file;
char *seq_id_plus = NULL;
char *seq = NULL;
size_t seq_storage_size;
size_t seq_len;
seq_lib *lib = create_empty_seq_lib();
if (NULL == lib) return NULL; /* ENOMEM */
if (setjmp(_jmp_buf) != 0)
return NULL; /* If we get here, there was an error in
p3sl_safe_malloc or p3sl_safe_realloc. */
lib->repeat_file = (char*) p3sl_safe_malloc(strlen(filename) + 1);
strcpy(lib->repeat_file, filename);
if((file = fopen(lib->repeat_file,"r")) == NULL) {
p3sl_append_new_chunk(&lib->error,
"Cannot open ");
goto ERROR;
}
seq = (char*) p3sl_safe_malloc(P3SL_INIT_BUF_SIZE);
seq_storage_size = P3SL_INIT_BUF_SIZE;
seq_len = 0;
*seq = '\0';
/* Read in the lines from the file */
while(1) {
p = p3_read_line(file);
if (NULL == p) {
/* End of file */
if (seq_id_plus != NULL) {
if (seq_len == 0) {
p3sl_append_new_chunk(&lib->error,
"Empty sequence in ");
goto ERROR;
} else {
if (add_seq_to_seq_lib(lib, seq, seq_id_plus, errfrag)) {
p3sl_append(&lib->error, " in ");
goto ERROR;
}
}
free(seq_id_plus);
seq_id_plus = NULL;
}
break;
}
if ('>' == *p) {
/* We found an id line */
/* There are two possibilities */
if (seq_id_plus == NULL) {
/* 1. This is the first id line in the file,
in which case seq_id_plus == NULL
(and seq_len == 0). */
seq_id_plus = (char*) p3sl_safe_malloc(strlen(p) + 1);
p++; /* skip past the '>' */
strcpy(seq_id_plus, p);
} else {
/* 2. This is NOT the first id line in the
file, in which case seq_id_plus != NULL */
if (seq_id_plus != NULL) {
if (seq_len == 0) {
p3sl_append_new_chunk(&lib->error,
"Empty sequence in ");
goto ERROR;
} else {
if (add_seq_to_seq_lib(lib, seq, seq_id_plus, errfrag)) {
p3sl_append(&lib->error, " in ");
goto ERROR;
}
/*"emtpy" the buffer */
seq_len = 0;
*seq = '\0';
}
free(seq_id_plus);
seq_id_plus = (char*) p3sl_safe_malloc(strlen(p));
p++; /* skip past the '>' */
strcpy(seq_id_plus, p);
}
}
} else {
/* A sequence line */
if (seq_id_plus == NULL) {
p3sl_append_new_chunk(&lib->error,
"Missing id line (expected '>') in ");
goto ERROR;
}
while ( strlen(p)+ seq_len + 1 > seq_storage_size ) {
seq_storage_size *= 2;
seq = (char*) p3sl_safe_realloc(seq, seq_storage_size);
}
strcat(seq, p);
seq_len += strlen(p);
}
}
if (lib->seq_num == 0) {
p3sl_append_new_chunk(&lib->error, "Empty ");
goto ERROR;
}
reverse_complement_seq_lib(lib);
if (file) fclose(file);
free(seq);
free(seq_id_plus);
return lib;
ERROR:
free(seq);
free(seq_id_plus);
p3sl_append(&lib->error, errfrag);
p3sl_append(&lib->error, " ");
p3sl_append(&lib->error, lib->repeat_file);
if (file) fclose(file);
return lib;
}
int
read_p3_file(const char *file_name,
const p3_file_type expected_file_type,
int echo_output,
int strict_tags,
p3_global_settings *pa,
seq_args *sa,
pr_append_str *fatal_err,
pr_append_str *nonfatal_err,
pr_append_str *warnings,
read_boulder_record_results *read_boulder_record_res)
{
FILE *file;
int ret_par = 0;
int io_version = 4;
char *line1;
char *line2;
char *line3;
p3_file_type file_type = all_parameters;
/* Check if a file name was provided */
PR_ASSERT(NULL != file_name);
/* Open the file */
if (!(file = fopen(file_name,"r"))) {
pr_append2(fatal_err, "Cannot open ", file_name);
return ret_par;
}
/* Parse and interpret the first 3 lines */
/* Line 1 */
line1 = p3_read_line(file);
if (!line1) {
pr_append2(fatal_err,
"Settings file is empty: ",
file_name);
return ret_par;
}
if (strcmp(line1,
"Primer3 File - http://primer3.sourceforge.net")) {
pr_append2(fatal_err,
"First line must be \"Primer3 File - http://primer3.sourceforge.net\" in ",
file_name);
return ret_par;
}
/* Line 2 */
line2 = p3_read_line(file);
if (!line2) {
pr_append2(fatal_err,
"Incorrect file format (too few lines) in ",
file_name);
return ret_par;
}
if (!strcmp(line2,"P3_FILE_TYPE=all_parameters")) {
file_type = all_parameters;
} else if (!strcmp(line2,"P3_FILE_TYPE=sequence")) {
file_type = sequence;
} else if (!strcmp(line2,"P3_FILE_TYPE=settings")) {
file_type = settings;
} else {
pr_append2(fatal_err,
"Unknown file type in at line 2 (line2='", line2);
pr_append(fatal_err, "') in ");
pr_append(fatal_err, file_name);
return ret_par;
}
if (echo_output) {
printf("P3_SETTINGS_FILE_USED=%s\n", file_name);
printf("%s\n", line2);
}
/* Line 3 */
line3 = p3_read_line(file);
if (!line3) {
pr_append2(fatal_err,
"Incorrect file format (too few lines) in ",
file_name);
return ret_par;
}
if (strcmp(line3, "")) {
pr_append2(fatal_err, "Line 3 must be empty in ",
file_name);
return ret_par;
}
/* Check if the file type matches the expected type */
if (file_type != expected_file_type){
pr_append_new_chunk(nonfatal_err,
"Unexpected P3 file type parsed");
}
/* read the file */
ret_par = read_boulder_record(file, &strict_tags, &io_version,
echo_output, expected_file_type,
pa, sa, fatal_err,
nonfatal_err, warnings,
read_boulder_record_res);
if (echo_output) printf("P3_SETTINGS_FILE_END=\n");
if (file) fclose(file);
return ret_par;
}
/*
* See read_boulder.h for description.
*/
int
read_record(FILE *file_input,
const int *strict_tags,
const int *io_version,
int echo_output,
const p3_file_type read_file_type,
p3_global_settings *pa,
seq_args *sa,
pr_append_str *glob_err, /* Really should be called fatal_parse_err */
pr_append_str *nonfatal_parse_err) {
int line_len; /* seq_len; n_quality; */
int tag_len, datum_len;
int data_found = 0;
p3_file_type file_type = all_parameters;
int pick_internal_oligo = 2;
char *s, *n, *datum, *task_tmp = NULL;
const char *p;
pr_append_str *parse_err;
pr_append_str *non_fatal_err;
char *repeat_file_path = NULL, *int_repeat_file_path = NULL;
/* FIX ME call p3_create_seq_args inside read_boulder? */
non_fatal_err = nonfatal_parse_err;
while ((s = p3_read_line(file_input)) != NULL && strcmp(s,"=")) {
/* Deal with the file headers */
if ((strcmp(s,"Primer3 File - http://primer3.sourceforge.net")) == 0) {
/* read FILE_TYPE */
if ((s = p3_read_line(file_input)) == NULL && !(strcmp(s,"=")))
break;
if ((strcmp(s,"P3_FILE_TYPE=all_parameters")) == 0) {
file_type = all_parameters;
}
else if ((strcmp(s,"P3_FILE_TYPE=sequence")) == 0) {
file_type = sequence;
}
else if ((strcmp(s,"P3_FILE_TYPE=settings")) == 0) {
file_type = settings;
}
else {
pr_append_new_chunk(glob_err, "Unknown P3_FILE_TYPE");
}
/* read the empty line */
if ((s = p3_read_line(file_input)) == NULL && !(strcmp(s,"=")))
break;
/* Check if the file type matches the expected type */
if (file_type != read_file_type && echo_output){
pr_append_new_chunk(nonfatal_parse_err,
"Unexpected P3 file type parsed");
}
continue;
}
/* Read only the PRIMER tags if settings is selected */
if (read_file_type == settings && strncmp(s, "PRIMER_", 7)
&& strncmp(s, "P3_FILE_ID", 10)) {
continue;
}
/* Silently ignore all primer3plus tags */
if (!(strncmp(s, "P3P_", 4))) {
continue;
}
data_found = 1;
/* Print out the input */
if (echo_output) printf("%s\n", s);
line_len = strlen(s);
/* If the line has an "=" read the tag in the right place */
if ((n=strchr(s,'=')) == NULL) {
/* The input line is illegal because it has no
* "=" in it, but we still will read to the end
* of the record. */
pr_append_new_chunk(glob_err, "Input line with no '=': ");
pr_append(glob_err, s);
} else {
/* Get the tag and the value pointers */
tag_len = n - s;
datum = n + 1;
datum_len = line_len - tag_len - 1;
/* Process "Sequence" (i.e. Per-Record) Arguments". */
parse_err = non_fatal_err;
/* Process the old sequence Tags*/
if (*io_version == 0) {
/* COMPARE_AND_MALLOC("SEQUENCE", sa->sequence); */
if (COMPARE("SEQUENCE")) { /* NEW WAY */
if (/* p3_get_seq_arg_sequence(sa) */ sa->sequence) {
pr_append_new_chunk(parse_err, "Duplicate tag: ");
pr_append(parse_err, "SEQUENCE");
} else {
if (p3_set_sa_sequence(sa, datum)) exit(-2);
}
continue;
}
if (COMPARE("PRIMER_SEQUENCE_QUALITY")) {
if ((sa->n_quality = parse_seq_quality(datum, &sa->quality)) == 0) {
pr_append_new_chunk(parse_err,
"Error in sequence quality data");
/* continue; // FIX ME superfluous ? */
}
continue;
}
COMPARE_AND_MALLOC("PRIMER_SEQUENCE_ID", sa->sequence_name);
COMPARE_AND_MALLOC("MARKER_NAME", sa->sequence_name);
COMPARE_AND_MALLOC("PRIMER_LEFT_INPUT", sa->left_input);
COMPARE_AND_MALLOC("PRIMER_RIGHT_INPUT", sa->right_input);
COMPARE_AND_MALLOC("PRIMER_INTERNAL_OLIGO_INPUT", sa->internal_input);
COMPARE_INTERVAL_LIST("TARGET", &sa->tar2);
COMPARE_INTERVAL_LIST("EXCLUDED_REGION", &sa->excl2);
COMPARE_INTERVAL_LIST("PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION",
&sa->excl_internal2);
if (COMPARE("INCLUDED_REGION")) {
p = parse_int_pair("INCLUDED_REGION", datum, ',',
&sa->incl_s, &sa->incl_l, parse_err);
if (NULL == p) /*
* An error; the message is already
* in parse_err.
*/
continue;
while (' ' == *p || '\t' == *p) p++;
if (*p != '\n' && *p != '\0')
tag_syntax_error("INCLUDED_REGION", datum,
parse_err);
continue;
}
COMPARE_INT("PRIMER_START_CODON_POSITION", sa->start_codon_pos);
}
/* Process the new sequence Tags*/
else {
/* COMPARE_AND_MALLOC("SEQUENCE", sa->sequence); */
if (COMPARE("SEQUENCE_DNA")) { /* NEW WAY */
if (/* p3_get_seq_arg_sequence(sa) */ sa->sequence) {
pr_append_new_chunk(parse_err, "Duplicate tag: ");
pr_append(parse_err, "SEQUENCE_DNA");
} else {
if (p3_set_sa_sequence(sa, datum)) exit(-2);
}
continue;
}
if (COMPARE("SEQUENCE_QUALITY")) {
if ((sa->n_quality = parse_seq_quality(datum, &sa->quality)) == 0) {
pr_append_new_chunk(parse_err,
"Error in sequence quality data");
/* continue; // FIX ME superfluous ? */
}
continue;
}
COMPARE_AND_MALLOC("SEQUENCE_ID", sa->sequence_name);
COMPARE_AND_MALLOC("SEQUENCE_PRIMER", sa->left_input);
COMPARE_AND_MALLOC("SEQUENCE_PRIMER_REVCOMP", sa->right_input);
COMPARE_AND_MALLOC("SEQUENCE_OLIGO", sa->internal_input);
COMPARE_INTERVAL_LIST("SEQUENCE_TARGET", &sa->tar2);
COMPARE_INTERVAL_LIST("SEQUENCE_EXCLUDED_REGION", &sa->excl2);
COMPARE_INTERVAL_LIST("SEQUENCE_INTERNAL_EXCLUDED_REGION",
&sa->excl_internal2);
if (COMPARE("SEQUENCE_INCLUDED_REGION")) {
p = parse_int_pair("SEQUENCE_INCLUDED_REGION", datum, ',',
&sa->incl_s, &sa->incl_l, parse_err);
if (NULL == p) /*
* An error; the message is already
* in parse_err.
*/
continue;
while (' ' == *p || '\t' == *p) p++;
if (*p != '\n' && *p != '\0')
tag_syntax_error("SEQUENCE_INCLUDED_REGION", datum,
parse_err);
continue;
}
COMPARE_INT("SEQUENCE_START_CODON_POSITION", sa->start_codon_pos);
}
/*
* Process "Global" Arguments (those that persist between boulder
* records).
*/
parse_err = glob_err; /* These errors are considered fatal. */
if (COMPARE("PRIMER_PRODUCT_SIZE_RANGE")
|| COMPARE("PRIMER_DEFAULT_PRODUCT")) {
parse_product_size("PRIMER_PRODUCT_SIZE_RANGE", datum, pa,
parse_err);
continue;
}
COMPARE_INT("PRIMER_DEFAULT_SIZE", pa->p_args.opt_size);
COMPARE_INT("PRIMER_OPT_SIZE", pa->p_args.opt_size);
COMPARE_INT("PRIMER_MIN_SIZE", pa->p_args.min_size);
COMPARE_INT("PRIMER_MAX_SIZE", pa->p_args.max_size);
COMPARE_INT("PRIMER_MAX_POLY_X", pa->p_args.max_poly_x);
COMPARE_FLOAT("PRIMER_OPT_TM", pa->p_args.opt_tm);
COMPARE_FLOAT("PRIMER_OPT_GC_PERCENT", pa->p_args.opt_gc_content);
COMPARE_FLOAT("PRIMER_MIN_TM", pa->p_args.min_tm);
COMPARE_FLOAT("PRIMER_MAX_TM", pa->p_args.max_tm);
COMPARE_FLOAT("PRIMER_MAX_DIFF_TM", pa->max_diff_tm);
if (*io_version == 0) {
COMPARE_INT("PRIMER_TM_SANTALUCIA", pa->tm_santalucia); /* added by T.Koressaar */
} else {
COMPARE_INT("PRIMER_TM_FORMULA", pa->tm_santalucia); /* added by T.Koressaar */
}
COMPARE_INT("PRIMER_SALT_CORRECTIONS", pa->salt_corrections); /* added by T.Koressaar */
COMPARE_FLOAT("PRIMER_MIN_GC", pa->p_args.min_gc);
COMPARE_FLOAT("PRIMER_MAX_GC", pa->p_args.max_gc);
/* begin of added by T.Koressaar: */
if (*io_version == 0) {
COMPARE_FLOAT("PRIMER_SALT_CONC", pa->p_args.salt_conc);
COMPARE_FLOAT("PRIMER_DIVALENT_CONC", pa->p_args.divalent_conc);
} else {
COMPARE_FLOAT("PRIMER_SALT_MONOVALENT", pa->p_args.salt_conc);
COMPARE_FLOAT("PRIMER_SALT_DIVALENT", pa->p_args.divalent_conc);
}
COMPARE_FLOAT("PRIMER_DNTP_CONC", pa->p_args.dntp_conc);
/* end of added by T.Koressaar: */
COMPARE_FLOAT("PRIMER_DNA_CONC", pa->p_args.dna_conc);
COMPARE_INT("PRIMER_NUM_NS_ACCEPTED", pa->p_args.num_ns_accepted);
COMPARE_INT("PRIMER_PRODUCT_OPT_SIZE", pa->product_opt_size);
COMPARE_ALIGN_SCORE("PRIMER_SELF_ANY", pa->p_args.max_self_any);
COMPARE_ALIGN_SCORE("PRIMER_SELF_END", pa->p_args.max_self_end);
COMPARE_ALIGN_SCORE("PRIMER_PAIR_ANY", pa->pair_compl_any);
COMPARE_ALIGN_SCORE("PRIMER_PAIR_END", pa->pair_compl_end);
if (*io_version == 0) {
COMPARE_INT("PRIMER_FILE_FLAG", pa->file_flag);
} else {
COMPARE_INT("P3_FILE_FLAG", pa->file_flag);
}
COMPARE_INT("PRIMER_PICK_ANYWAY", pa->pick_anyway);
COMPARE_INT("PRIMER_GC_CLAMP", pa->gc_clamp);
COMPARE_INT("PRIMER_EXPLAIN_FLAG", pa->explain_flag);
COMPARE_INT("PRIMER_LIBERAL_BASE", pa->liberal_base);
COMPARE_INT("PRIMER_FIRST_BASE_INDEX", pa->first_base_index);
COMPARE_INT("PRIMER_NUM_RETURN", pa->num_return);
COMPARE_INT("PRIMER_MIN_QUALITY", pa->p_args.min_quality);
COMPARE_INT("PRIMER_MIN_END_QUALITY", pa->p_args.min_end_quality);
COMPARE_INT("PRIMER_MIN_THREE_PRIME_DISTANCE",
pa->min_three_prime_distance);
if (*io_version > 0 && file_type == settings) {
COMPARE_AND_MALLOC("P3_FILE_ID", pa->settings_file_id);
}
COMPARE_INT("PRIMER_QUALITY_RANGE_MIN", pa->quality_range_min);
COMPARE_INT("PRIMER_QUALITY_RANGE_MAX", pa->quality_range_max);
COMPARE_FLOAT("PRIMER_PRODUCT_MAX_TM", pa->product_max_tm);
COMPARE_FLOAT("PRIMER_PRODUCT_MIN_TM", pa->product_min_tm);
COMPARE_FLOAT("PRIMER_PRODUCT_OPT_TM", pa->product_opt_tm);
COMPARE_AND_MALLOC("PRIMER_TASK", task_tmp);
if (0 < *io_version) {
COMPARE_INT("PRIMER_PICK_RIGHT_PRIMER", pa->pick_right_primer);
COMPARE_INT("PRIMER_PICK_INTERNAL_OLIGO", pa->pick_internal_oligo);
COMPARE_INT("PRIMER_PICK_LEFT_PRIMER", pa->pick_left_primer);
}
else {
COMPARE_INT("PRIMER_PICK_INTERNAL_OLIGO", pick_internal_oligo);
}
COMPARE_INT("PRIMER_INTERNAL_OLIGO_OPT_SIZE", pa->o_args.opt_size);
COMPARE_INT("PRIMER_INTERNAL_OLIGO_MAX_SIZE", pa->o_args.max_size);
COMPARE_INT("PRIMER_INTERNAL_OLIGO_MIN_SIZE", pa->o_args.min_size);
COMPARE_INT("PRIMER_INTERNAL_OLIGO_MAX_POLY_X", pa->o_args.max_poly_x);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_OPT_TM", pa->o_args.opt_tm);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT",
pa->o_args.opt_gc_content);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_MAX_TM", pa->o_args.max_tm);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_MIN_TM", pa->o_args.min_tm);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_MIN_GC", pa->o_args.min_gc);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_MAX_GC", pa->o_args.max_gc);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_SALT_CONC", pa->o_args.salt_conc);
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_DIVALENT_CONC",
pa->o_args.divalent_conc); /* added by T.Koressaar */
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_DNTP_CONC",
pa->o_args.dntp_conc); /* added by T.Koressaar */
COMPARE_FLOAT("PRIMER_INTERNAL_OLIGO_DNA_CONC", pa->o_args.dna_conc);
COMPARE_INT("PRIMER_INTERNAL_OLIGO_NUM_NS", pa->o_args.num_ns_accepted);
COMPARE_INT("PRIMER_INTERNAL_OLIGO_MIN_QUALITY", pa->o_args.min_quality);
COMPARE_ALIGN_SCORE("PRIMER_INTERNAL_OLIGO_SELF_ANY",
pa->o_args.max_self_any);
COMPARE_ALIGN_SCORE("PRIMER_INTERNAL_OLIGO_SELF_END",
pa->o_args.max_self_end);
COMPARE_ALIGN_SCORE("PRIMER_MAX_MISPRIMING",
pa->p_args.max_repeat_compl);
COMPARE_ALIGN_SCORE("PRIMER_INTERNAL_OLIGO_MAX_MISHYB",
pa->o_args.max_repeat_compl);
COMPARE_ALIGN_SCORE("PRIMER_PAIR_MAX_MISPRIMING",
pa->pair_repeat_compl);
/* Mispriming / mishybing in the template. */
COMPARE_ALIGN_SCORE("PRIMER_MAX_TEMPLATE_MISPRIMING",
pa->p_args.max_template_mispriming);
COMPARE_ALIGN_SCORE("PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING",
pa->pair_max_template_mispriming);
COMPARE_ALIGN_SCORE("PRIMER_INTERNAL_OLIGO_MAX_TEMPLATE_MISHYB",
pa->o_args.max_template_mispriming);
/* Control interpretation of ambiguity codes in mispriming
and mishyb libraries. */
COMPARE_INT("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS",
pa->lib_ambiguity_codes_consensus);
COMPARE_FLOAT("PRIMER_INSIDE_PENALTY", pa->inside_penalty);
COMPARE_FLOAT("PRIMER_OUTSIDE_PENALTY", pa->outside_penalty);
if (COMPARE("PRIMER_MISPRIMING_LIBRARY")) {
if (repeat_file_path != NULL) {
pr_append_new_chunk(glob_err,
"Duplicate PRIMER_MISPRIMING_LIBRARY tag");
free(repeat_file_path);
repeat_file_path = NULL;
} else {
repeat_file_path = _rb_safe_malloc(strlen(datum) + 1);
strcpy(repeat_file_path, datum);
}
continue;
}
if (COMPARE("PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY")) {
if (int_repeat_file_path != NULL) {
pr_append_new_chunk(glob_err,
"Duplicate PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY tag");
free(int_repeat_file_path);
int_repeat_file_path = NULL;
} else {
int_repeat_file_path = _rb_safe_malloc(strlen(datum) + 1);
strcpy(int_repeat_file_path, datum);
}
continue;
}
if (COMPARE("PRIMER_COMMENT") || COMPARE("COMMENT")) continue;
COMPARE_FLOAT("PRIMER_MAX_END_STABILITY", pa->max_end_stability);
COMPARE_INT("PRIMER_LOWERCASE_MASKING",
pa->lowercase_masking); /* added by T. Koressaar */
/* weights for objective functions */
/* CHANGE TEMP/temp -> TM/tm */
COMPARE_FLOAT("PRIMER_WT_TM_GT", pa->p_args.weights.temp_gt);
COMPARE_FLOAT("PRIMER_WT_TM_LT", pa->p_args.weights.temp_lt);
COMPARE_FLOAT("PRIMER_WT_GC_PERCENT_GT", pa->p_args.weights.gc_content_gt);
COMPARE_FLOAT("PRIMER_WT_GC_PERCENT_LT", pa->p_args.weights.gc_content_lt);
COMPARE_FLOAT("PRIMER_WT_SIZE_LT", pa->p_args.weights.length_lt);
COMPARE_FLOAT("PRIMER_WT_SIZE_GT", pa->p_args.weights.length_gt);
COMPARE_FLOAT("PRIMER_WT_COMPL_ANY", pa->p_args.weights.compl_any);
COMPARE_FLOAT("PRIMER_WT_COMPL_END", pa->p_args.weights.compl_end);
COMPARE_FLOAT("PRIMER_WT_NUM_NS", pa->p_args.weights.num_ns);
COMPARE_FLOAT("PRIMER_WT_REP_SIM", pa->p_args.weights.repeat_sim);
COMPARE_FLOAT("PRIMER_WT_SEQ_QUAL", pa->p_args.weights.seq_quality);
COMPARE_FLOAT("PRIMER_WT_END_QUAL", pa->p_args.weights.end_quality);
COMPARE_FLOAT("PRIMER_WT_POS_PENALTY", pa->p_args.weights.pos_penalty);
COMPARE_FLOAT("PRIMER_WT_END_STABILITY",
pa->p_args.weights.end_stability);
COMPARE_FLOAT("PRIMER_WT_TEMPLATE_MISPRIMING",
pa->p_args.weights.template_mispriming);
COMPARE_FLOAT("PRIMER_IO_WT_TM_GT", pa->o_args.weights.temp_gt);
COMPARE_FLOAT("PRIMER_IO_WT_TM_LT", pa->o_args.weights.temp_lt);
COMPARE_FLOAT("PRIMER_IO_WT_GC_PERCENT_GT", pa->o_args.weights.gc_content_gt);
COMPARE_FLOAT("PRIMER_IO_WT_GC_PERCENT_LT", pa->o_args.weights.gc_content_lt);
COMPARE_FLOAT("PRIMER_IO_WT_SIZE_LT", pa->o_args.weights.length_lt);
COMPARE_FLOAT("PRIMER_IO_WT_SIZE_GT", pa->o_args.weights.length_gt);
COMPARE_FLOAT("PRIMER_IO_WT_COMPL_ANY", pa->o_args.weights.compl_any);
COMPARE_FLOAT("PRIMER_IO_WT_COMPL_END", pa->o_args.weights.compl_end);
COMPARE_FLOAT("PRIMER_IO_WT_NUM_NS", pa->o_args.weights.num_ns);
COMPARE_FLOAT("PRIMER_IO_WT_REP_SIM", pa->o_args.weights.repeat_sim);
COMPARE_FLOAT("PRIMER_IO_WT_SEQ_QUAL", pa->o_args.weights.seq_quality);
COMPARE_FLOAT("PRIMER_IO_WT_END_QUAL", pa->o_args.weights.end_quality);
COMPARE_FLOAT("PRIMER_IO_WT_TEMPLATE_MISHYB",
pa->o_args.weights.template_mispriming);
COMPARE_FLOAT("PRIMER_PAIR_WT_PR_PENALTY",
pa->pr_pair_weights.primer_quality);
COMPARE_FLOAT("PRIMER_PAIR_WT_IO_PENALTY",
pa->pr_pair_weights.io_quality);
COMPARE_FLOAT("PRIMER_PAIR_WT_DIFF_TM",
pa->pr_pair_weights.diff_tm);
COMPARE_FLOAT("PRIMER_PAIR_WT_COMPL_ANY",
pa->pr_pair_weights.compl_any);
COMPARE_FLOAT("PRIMER_PAIR_WT_COMPL_END",
pa->pr_pair_weights.compl_end);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_TM_LT",
pa->pr_pair_weights.product_tm_lt);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_TM_GT",
pa->pr_pair_weights.product_tm_gt);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_SIZE_GT",
pa->pr_pair_weights.product_size_gt);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_SIZE_LT",
pa->pr_pair_weights.product_size_lt);
COMPARE_FLOAT("PRIMER_PAIR_WT_REP_SIM",
pa->pr_pair_weights.repeat_sim);
COMPARE_FLOAT("PRIMER_PAIR_WT_TEMPLATE_MISPRIMING",
pa->pr_pair_weights.template_mispriming);
}
/* End of reading the tags in the right place */
/* Complain about unrecognized tags */
if (*strict_tags == 1) {
pr_append_new_chunk(glob_err, "Unrecognized tag: ");
pr_append(glob_err, s);
fprintf(stderr, "Unrecognized tag: %s\n", s);
}
} /* while ((s = p3_read_line(stdin)) != NULL && strcmp(s,"=")) { */
/* Check if the record was terminated by "=" */
if (NULL == s) { /* End of file. */
if (data_found) {
pr_append_new_chunk(glob_err,
"Final record not terminated by '='");
return 1;
} else return 0;
}
/* Figure out the right settings for the tasks*/
if (task_tmp != NULL) {
if (!strcmp_nocase(task_tmp, "pick_pcr_primers")) {
pa->primer_task = pick_detection_primers;
pa->pick_left_primer = 1;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 0;
} else if (!strcmp_nocase(task_tmp, "pick_pcr_primers_and_hyb_probe")) {
pa->primer_task = pick_detection_primers;
pa->pick_left_primer = 1;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 1;
} else if (!strcmp_nocase(task_tmp, "pick_left_only")) {
pa->primer_task = pick_detection_primers;
pa->pick_left_primer = 1;
pa->pick_right_primer = 0;
pa->pick_internal_oligo = 0;
} else if (!strcmp_nocase(task_tmp, "pick_right_only")) {
pa->primer_task = pick_detection_primers;
pa->pick_left_primer = 0;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 0;
} else if (!strcmp_nocase(task_tmp, "pick_hyb_probe_only")) {
pa->primer_task = pick_detection_primers;
pa->pick_left_primer = 0;
pa->pick_right_primer = 0;
pa->pick_internal_oligo = 1;
} else if (*io_version == 0) {
pr_append_new_chunk(glob_err, "Unrecognized PRIMER_TASK");
} else if (!strcmp_nocase(task_tmp, "pick_detection_primers")) {
pa->primer_task = pick_detection_primers;
} else if (!strcmp_nocase(task_tmp, "pick_cloning_primers")) {
pa->primer_task = pick_cloning_primers;
} else if (!strcmp_nocase(task_tmp, "pick_discriminative_primers")) {
pa->primer_task = pick_discriminative_primers;
} else if (!strcmp_nocase(task_tmp, "pick_sequencing_primers")) {
pa->primer_task = pick_sequencing_primers;
} else if (!strcmp_nocase(task_tmp, "pick_primer_list")) {
pa->primer_task = pick_primer_list;
} else if (!strcmp_nocase(task_tmp, "check_primers")) {
pa->primer_task = check_primers;
} else
pr_append_new_chunk(glob_err,
"Unrecognized PRIMER_TASK");
free(task_tmp);
}
/* WARNING: read_seq_lib uses p3_read_line, so repeat files cannot be read
* inside the while ((s = p3_read_line(stdin))...) loop above.
* FIX ME, in fact the reading of the library contents probably
* belongs inside primer3_boulder_main.c or libprimer3.c. */
/* Reading in the repeat libraries */
if (NULL != repeat_file_path) {
destroy_seq_lib(pa->p_args.repeat_lib);
if ('\0' == *repeat_file_path) {
/* Input now specifies no repeat library. */
pa->p_args.repeat_lib = NULL;
}
else {
pa->p_args.repeat_lib
= read_and_create_seq_lib(repeat_file_path,
"mispriming library");
if(pa->p_args.repeat_lib->error.data != NULL) {
pr_append_new_chunk(glob_err, pa->p_args.repeat_lib->error.data);
}
}
free(repeat_file_path);
repeat_file_path = NULL;
}
/* Reading in the repeat libraries for internal oligo */
if (NULL != int_repeat_file_path) {
destroy_seq_lib(pa->o_args.repeat_lib);
if ('\0' == *int_repeat_file_path) {
/* Input now specifies no mishybridization library. */
pa->o_args.repeat_lib = NULL;
}
else {
pa->o_args.repeat_lib =
read_and_create_seq_lib(int_repeat_file_path,
"internal oligo mishyb library");
if(pa->o_args.repeat_lib->error.data != NULL) {
pr_append_new_chunk(glob_err, pa->o_args.repeat_lib->error.data);
}
}
free(int_repeat_file_path);
int_repeat_file_path = NULL;
}
/* Fix very old tags for backward compatibility */
if (*io_version == 0) {
/* This next belongs here rather than libprimer3, because it deals
with potential incompatibility with old tags (kept for backward
compatibility, and new tags. */
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
/* Give a error if the tasks don't match */
if((pick_internal_oligo == 1 || pick_internal_oligo == 0) &&
(pa->primer_task == pick_left_only ||
pa->primer_task == pick_right_only ||
pa->primer_task == pick_hyb_probe_only)) {
pr_append_new_chunk(glob_err,
"Contradiction in primer_task definition");
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
} else if (pick_internal_oligo == 1) {
pa->pick_left_primer = 1;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 1;
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
} else if (pick_internal_oligo == 0) {
pa->pick_left_primer = 1;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 0;
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
}
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
}
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
return 1;
}
/*
* See read_boulder.h for description.
*/
int
read_boulder_record(FILE *file_input,
const int *strict_tags,
const int *io_version,
int echo_output, /* should be echo_input */
const p3_file_type file_type,
p3_global_settings *pa,
seq_args *sa,
pr_append_str *glob_err, /* Really should be called fatal_parse_err */
pr_append_str *nonfatal_parse_err,
pr_append_str *warnings,
read_boulder_record_results *res)
{
int line_len;
int tag_len, datum_len;
int data_found = 0;
char *s, *n, *datum, *task_tmp = NULL;
const char *p;
pr_append_str *parse_err;
pr_append_str *non_fatal_err;
char *repeat_file_path = NULL, *int_repeat_file_path = NULL;
int tmp_int;
/* int min_3_prime = 0, min_5_prime = 0; Removed 10/20/2010 */
int min_3_prime_distance_global = 0; /* needed to check if both global and specific*/
int min_3_prime_distance_specific = 0; /* are given in same boulder record */
int min_three_prime_distance; /* holder for the value of this tag */
double tmp_double;
non_fatal_err = nonfatal_parse_err;
while (((s = p3_read_line(file_input)) != NULL) && (strcmp(s,"="))) {
/* If we are reading from a settings file, then skip every
line except those begining "PRIMER_" or "P3_FILE_ID".
Hint: strncomp returns 0 if both strings are equal */
if (file_type == settings
&& strncmp(s, "PRIMER_", 7) /* "s does not begin with 'PRIMER_'" */
&& strncmp(s, "P3_FILE_ID", 10) /* "s does not begin with
'P3_FILE_ID'" */
) {
continue;
}
/* Silently ignore all primer3plus tags */
/* Removed 10/20/10 because P3P_ tags
are already ignored in settings files. */
/* if (!(strncmp(s, "P3P_", 4))) {
continue;
} */
data_found = 1;
/* Print out the input */
if (echo_output) printf("%s\n", s);
line_len = strlen(s);
/* If the line has an "=" read the tag in the right place */
if ((n=strchr(s,'=')) == NULL) {
/* The input line is illegal because it has no
* "=" in it, but we still will read to the end
* of the record. */
pr_append_new_chunk(glob_err, "Input line with no '=': ");
pr_append(glob_err, s);
continue;
}
/* Read in the new tags used from primer3 version 2.0 on */
else {
/* Get the tag and the value pointers */
tag_len = n - s;
datum = n + 1;
datum_len = line_len - tag_len - 1;
/* Process "Sequence" (i.e. Per-Record) Arguments". */
parse_err = non_fatal_err;
/* COMPARE_AND_MALLOC("SEQUENCE", sa->sequence); */
if (COMPARE("SEQUENCE_TEMPLATE")) { /* NEW WAY */
if (/* p3_get_seq_arg_sequence(sa) */ sa->sequence) {
pr_append_new_chunk(parse_err, "Duplicate tag: ");
pr_append(parse_err, "SEQUENCE_TEMPLATE");
} else {
if (p3_set_sa_sequence(sa, datum)) exit(-2);
}
continue;
}
if (COMPARE("SEQUENCE_QUALITY")) {
if ((sa->n_quality = parse_seq_quality(datum, sa)) == 0) {
pr_append_new_chunk(parse_err,
"Error in sequence quality data");
}
continue;
}
COMPARE_AND_MALLOC("SEQUENCE_ID", sa->sequence_name);
COMPARE_AND_MALLOC("SEQUENCE_PRIMER", sa->left_input);
COMPARE_AND_MALLOC("SEQUENCE_PRIMER_REVCOMP", sa->right_input);
COMPARE_AND_MALLOC("SEQUENCE_INTERNAL_OLIGO", sa->internal_input);
COMPARE_2_INTERVAL_LIST("SEQUENCE_PRIMER_PAIR_OK_REGION_LIST", &sa->ok_regions);
COMPARE_INTERVAL_LIST("SEQUENCE_TARGET", &sa->tar2);
COMPARE_INTERVAL_LIST("SEQUENCE_EXCLUDED_REGION", &sa->excl2);
COMPARE_INTERVAL_LIST("SEQUENCE_INTERNAL_EXCLUDED_REGION",
&sa->excl_internal2);
if (COMPARE("SEQUENCE_OVERLAP_JUNCTION_LIST")) {
if (parse_intron_list(datum, sa->primer_overlap_junctions,
&sa->primer_overlap_junctions_count) == 0) {
pr_append_new_chunk(parse_err,
"Error in SEQUENCE_PRIMER_OVERLAP_JUNCTION_LIST");
}
continue;
}
if (COMPARE("SEQUENCE_INCLUDED_REGION")) {
p = parse_int_pair("SEQUENCE_INCLUDED_REGION", datum, ',',
&sa->incl_s, &sa->incl_l, parse_err);
if (NULL == p) /* An error; the message is already
* in parse_err. */
continue;
while (' ' == *p || '\t' == *p) p++;
if (*p != '\n' && *p != '\0')
tag_syntax_error("SEQUENCE_INCLUDED_REGION", datum,
parse_err);
continue;
}
COMPARE_INT("SEQUENCE_START_CODON_POSITION", sa->start_codon_pos);
COMPARE_INT("SEQUENCE_FORCE_LEFT_START", sa->force_left_start);
COMPARE_INT("SEQUENCE_FORCE_LEFT_END", sa->force_left_end);
COMPARE_INT("SEQUENCE_FORCE_RIGHT_START", sa->force_right_start);
COMPARE_INT("SEQUENCE_FORCE_RIGHT_END", sa->force_right_end);
/* Process "Global" Arguments (those that persist between boulder
* records). */
parse_err = glob_err; /* These errors are considered fatal. */
if (COMPARE("PRIMER_PRODUCT_SIZE_RANGE")) {
parse_product_size("PRIMER_PRODUCT_SIZE_RANGE", datum, pa,
parse_err);
continue;
}
COMPARE_INT("PRIMER_OPT_SIZE", pa->p_args.opt_size);
COMPARE_INT("PRIMER_MIN_SIZE", pa->p_args.min_size);
COMPARE_INT("PRIMER_MAX_SIZE", pa->p_args.max_size);
COMPARE_INT("PRIMER_MAX_POLY_X", pa->p_args.max_poly_x);
COMPARE_FLOAT("PRIMER_OPT_TM", pa->p_args.opt_tm);
COMPARE_FLOAT("PRIMER_OPT_GC_PERCENT", pa->p_args.opt_gc_content);
COMPARE_FLOAT("PRIMER_MIN_TM", pa->p_args.min_tm);
COMPARE_FLOAT("PRIMER_MAX_TM", pa->p_args.max_tm);
COMPARE_FLOAT("PRIMER_PAIR_MAX_DIFF_TM", pa->max_diff_tm);
if (COMPARE("PRIMER_TM_FORMULA")) {
parse_int("PRIMER_TM_FORMULA", datum, &tmp_int, parse_err);
pa->tm_santalucia = (tm_method_type) tmp_int; /* added by T.Koressaar */
continue;
}
if (COMPARE("PRIMER_SALT_CORRECTIONS")) {
parse_int("PRIMER_SALT_CORRECTIONS", datum, &tmp_int, parse_err);
pa->salt_corrections = (salt_correction_type) tmp_int; /* added by T.Koressaar */
continue;
}
COMPARE_FLOAT("PRIMER_MIN_GC", pa->p_args.min_gc);
COMPARE_FLOAT("PRIMER_MAX_GC", pa->p_args.max_gc);
COMPARE_FLOAT("PRIMER_SALT_MONOVALENT", pa->p_args.salt_conc);
COMPARE_FLOAT("PRIMER_SALT_DIVALENT", pa->p_args.divalent_conc);
COMPARE_FLOAT("PRIMER_DNTP_CONC", pa->p_args.dntp_conc);
COMPARE_FLOAT("PRIMER_DNA_CONC", pa->p_args.dna_conc);
COMPARE_INT("PRIMER_MAX_NS_ACCEPTED", pa->p_args.num_ns_accepted);
COMPARE_INT("PRIMER_PRODUCT_OPT_SIZE", pa->product_opt_size);
COMPARE_FLOAT("PRIMER_MAX_SELF_ANY", pa->p_args.max_self_any);
/* COMPARE_FLOAT("PRIMER_MAX_SELF_END", pa->p_args.max_self_end); */
/* NEW */ COMPARE_FLOAT_USE_FN("PRIMER_MAX_SELF_END", p3_set_gs_primer_self_end)
/* if (COMPARE("PRIMER_MAX_SELF_END")) {
parse_double("PRIMER_MAX_SELF_END", datum, &tmp_double, parse_err);
p3_set_gs_primer_self_end(pa, tmp_double);
continue;
} */
COMPARE_FLOAT("PRIMER_MAX_SELF_ANY_TH", pa->p_args.max_self_any_th);
COMPARE_FLOAT("PRIMER_MAX_SELF_END_TH", pa->p_args.max_self_end_th);
COMPARE_FLOAT("PRIMER_MAX_HAIRPIN_TH", pa->p_args.max_hairpin_th);
COMPARE_FLOAT("PRIMER_PAIR_MAX_COMPL_ANY", pa->pair_compl_any);
COMPARE_FLOAT("PRIMER_PAIR_MAX_COMPL_END", pa->pair_compl_end);
COMPARE_FLOAT("PRIMER_PAIR_MAX_COMPL_ANY_TH", pa->pair_compl_any_th);
COMPARE_FLOAT("PRIMER_PAIR_MAX_COMPL_END_TH", pa->pair_compl_end_th);
COMPARE_INT("P3_FILE_FLAG", res->file_flag);
COMPARE_INT("PRIMER_PICK_ANYWAY", pa->pick_anyway);
COMPARE_INT("PRIMER_GC_CLAMP", pa->gc_clamp);
COMPARE_INT("PRIMER_MAX_END_GC", pa->max_end_gc);
COMPARE_INT("PRIMER_EXPLAIN_FLAG", res->explain_flag);
COMPARE_INT("PRIMER_LIBERAL_BASE", pa->liberal_base);
COMPARE_INT("PRIMER_FIRST_BASE_INDEX", pa->first_base_index);
COMPARE_INT("PRIMER_NUM_RETURN", pa->num_return);
COMPARE_INT("PRIMER_MIN_QUALITY", pa->p_args.min_quality);
COMPARE_INT("PRIMER_MIN_END_QUALITY", pa->p_args.min_end_quality);
if (COMPARE("PRIMER_MIN_THREE_PRIME_DISTANCE")) {
parse_int("PRIMER_MIN_THREE_PRIME_DISTANCE", datum, &(min_three_prime_distance), parse_err);
/* check if specific tag also specified - error in this case */
if (min_3_prime_distance_specific == 1) {
pr_append_new_chunk(glob_err,
"Both PRIMER_MIN_THREE_PRIME_DISTANCE and PRIMER_{LEFT/RIGHT}_MIN_THREE_PRIME_DISTANCE specified");
} else {
min_3_prime_distance_global = 1;
/* set up individual flags */
pa->min_left_three_prime_distance = min_three_prime_distance;
pa->min_right_three_prime_distance = min_three_prime_distance;
}
continue;
}
if (COMPARE("PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE")) {
parse_int("PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE", datum, &(pa->min_left_three_prime_distance), parse_err);
/* check if global tag also specified - error in this case */
if (min_3_prime_distance_global == 1) {
pr_append_new_chunk(glob_err,
"Both PRIMER_MIN_THREE_PRIME_DISTANCE and PRIMER_{LEFT/RIGHT}_MIN_THREE_PRIME_DISTANCE specified");
} else {
min_3_prime_distance_specific = 1;
}
continue;
}
if (COMPARE("PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE")) {
parse_int("PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE", datum, &(pa->min_right_three_prime_distance), parse_err);
/* check if global tag also specified - error in this case */
if (min_3_prime_distance_global == 1) {
pr_append_new_chunk(glob_err,
"Both PRIMER_MIN_THREE_PRIME_DISTANCE and PRIMER_{LEFT/RIGHT}_MIN_THREE_PRIME_DISTANCE specified");
} else {
min_3_prime_distance_specific = 1;
}
continue;
}
if (file_type == settings) {
if (COMPARE("P3_FILE_ID")) continue;
}
COMPARE_INT("PRIMER_QUALITY_RANGE_MIN", pa->quality_range_min);
COMPARE_INT("PRIMER_QUALITY_RANGE_MAX", pa->quality_range_max);
COMPARE_FLOAT("PRIMER_PRODUCT_MAX_TM", pa->product_max_tm);
COMPARE_FLOAT("PRIMER_PRODUCT_MIN_TM", pa->product_min_tm);
COMPARE_FLOAT("PRIMER_PRODUCT_OPT_TM", pa->product_opt_tm);
COMPARE_INT("PRIMER_SEQUENCING_LEAD", pa->sequencing.lead);
COMPARE_INT("PRIMER_SEQUENCING_SPACING", pa->sequencing.spacing);
COMPARE_INT("PRIMER_SEQUENCING_INTERVAL", pa->sequencing.interval);
COMPARE_INT("PRIMER_SEQUENCING_ACCURACY", pa->sequencing.accuracy);
if (COMPARE("PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION")) {
parse_int("PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION", datum, &pa->min_5_prime_overlap_of_junction, parse_err);
/* min_5_prime = 1; Removed 10/20/2010 */
continue;
}
if (COMPARE("PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION")) {
parse_int("PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION", datum, &pa->min_3_prime_overlap_of_junction, parse_err);
/* min_3_prime = 1; Removed 10/20/2010 */
continue;
}
COMPARE_AND_MALLOC("PRIMER_TASK", task_tmp);
COMPARE_INT("PRIMER_PICK_RIGHT_PRIMER", pa->pick_right_primer);
COMPARE_INT("PRIMER_PICK_INTERNAL_OLIGO", pa->pick_internal_oligo);
COMPARE_INT("PRIMER_PICK_LEFT_PRIMER", pa->pick_left_primer);
COMPARE_INT("PRIMER_INTERNAL_OPT_SIZE", pa->o_args.opt_size);
COMPARE_INT("PRIMER_INTERNAL_MAX_SIZE", pa->o_args.max_size);
COMPARE_INT("PRIMER_INTERNAL_MIN_SIZE", pa->o_args.min_size);
COMPARE_INT("PRIMER_INTERNAL_MAX_POLY_X", pa->o_args.max_poly_x);
COMPARE_FLOAT("PRIMER_INTERNAL_OPT_TM", pa->o_args.opt_tm);
COMPARE_FLOAT("PRIMER_INTERNAL_OPT_GC_PERCENT",
pa->o_args.opt_gc_content);
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_TM", pa->o_args.max_tm);
COMPARE_FLOAT("PRIMER_INTERNAL_MIN_TM", pa->o_args.min_tm);
COMPARE_FLOAT("PRIMER_INTERNAL_MIN_GC", pa->o_args.min_gc);
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_GC", pa->o_args.max_gc);
COMPARE_FLOAT("PRIMER_INTERNAL_SALT_MONOVALENT",
pa->o_args.salt_conc);
COMPARE_FLOAT("PRIMER_INTERNAL_SALT_DIVALENT",
pa->o_args.divalent_conc);
COMPARE_FLOAT("PRIMER_INTERNAL_DNTP_CONC",
pa->o_args.dntp_conc);
COMPARE_FLOAT("PRIMER_INTERNAL_DNA_CONC", pa->o_args.dna_conc);
COMPARE_INT("PRIMER_INTERNAL_MAX_NS_ACCEPTED", pa->o_args.num_ns_accepted);
COMPARE_INT("PRIMER_INTERNAL_MIN_QUALITY", pa->o_args.min_quality);
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_SELF_ANY",
pa->o_args.max_self_any);
/* COMPARE_FLOAT("PRIMER_INTERNAL_MAX_SELF_END",
pa->o_args.max_self_end); */
/* NEW */ COMPARE_FLOAT_USE_FN("PRIMER_INTERNAL_MAX_SELF_END",
p3_set_gs_primer_internal_oligo_self_end);
/* if (COMPARE("PRIMER_INTERNAL_MAX_SELF_END")) {
parse_double("PRIMER_INTERNAL_MAX_SELF_END", datum, &tmp_double, parse_err);
p3_set_gs_primer_internal_oligo_self_end(pa, tmp_double);
continue;
} */
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_SELF_ANY_TH",
pa->o_args.max_self_any_th);
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_SELF_END_TH",
pa->o_args.max_self_end_th);
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_HAIRPIN_TH",
pa->o_args.max_hairpin_th);
COMPARE_FLOAT("PRIMER_MAX_LIBRARY_MISPRIMING",
pa->p_args.max_repeat_compl);
COMPARE_FLOAT("PRIMER_INTERNAL_MAX_LIBRARY_MISHYB",
pa->o_args.max_repeat_compl);
COMPARE_FLOAT("PRIMER_PAIR_MAX_LIBRARY_MISPRIMING",
pa->pair_repeat_compl);
/* Mispriming / mishybing in the template. */
COMPARE_FLOAT("PRIMER_MAX_TEMPLATE_MISPRIMING",
pa->p_args.max_template_mispriming);
COMPARE_FLOAT("PRIMER_MAX_TEMPLATE_MISPRIMING_TH",
pa->p_args.max_template_mispriming_th);
COMPARE_FLOAT("PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING",
pa->pair_max_template_mispriming);
COMPARE_FLOAT("PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH",
pa->pair_max_template_mispriming_th);
/* Control interpretation of ambiguity codes in mispriming
and mishyb libraries. */
COMPARE_INT("PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS",
pa->lib_ambiguity_codes_consensus);
COMPARE_FLOAT("PRIMER_INSIDE_PENALTY", pa->inside_penalty);
COMPARE_FLOAT("PRIMER_OUTSIDE_PENALTY", pa->outside_penalty);
if (COMPARE("PRIMER_MISPRIMING_LIBRARY")) {
if (repeat_file_path != NULL) {
pr_append_new_chunk(glob_err,
"Duplicate PRIMER_MISPRIMING_LIBRARY tag");
free(repeat_file_path);
repeat_file_path = NULL;
} else {
repeat_file_path = (char*) _rb_safe_malloc(strlen(datum) + 1);
strcpy(repeat_file_path, datum);
}
continue;
}
if (COMPARE("PRIMER_INTERNAL_MISHYB_LIBRARY")) {
if (int_repeat_file_path != NULL) {
pr_append_new_chunk(glob_err,
"Duplicate PRIMER_INTERNAL_MISHYB_LIBRARY tag");
free(int_repeat_file_path);
int_repeat_file_path = NULL;
} else {
int_repeat_file_path = (char*) _rb_safe_malloc(strlen(datum) + 1);
strcpy(int_repeat_file_path, datum);
}
continue;
}
if (COMPARE("P3_COMMENT")) continue;
COMPARE_FLOAT("PRIMER_MAX_END_STABILITY", pa->max_end_stability);
COMPARE_INT("PRIMER_LOWERCASE_MASKING",
pa->lowercase_masking);
/* added by T. Koressaar */
OVERWRITE_COMPARE_AND_MALLOC("PRIMER_MUST_MATCH_FIVE_PRIME", pa->p_args.must_match_five_prime);
OVERWRITE_COMPARE_AND_MALLOC("PRIMER_MUST_MATCH_THREE_PRIME", pa->p_args.must_match_three_prime);
OVERWRITE_COMPARE_AND_MALLOC("PRIMER_INTERNAL_MUST_MATCH_FIVE_PRIME", pa->o_args.must_match_five_prime);
OVERWRITE_COMPARE_AND_MALLOC("PRIMER_INTERNAL_MUST_MATCH_THREE_PRIME", pa->o_args.must_match_three_prime);
/* added by A. Untergasser */
COMPARE_INT("PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT", pa->thermodynamic_oligo_alignment);
COMPARE_INT("PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT", pa->thermodynamic_template_alignment);
if (COMPARE("PRIMER_THERMODYNAMIC_PARAMETERS_PATH")) {
if (thermodynamic_params_path == NULL) {
thermodynamic_params_path = (char*) _rb_safe_malloc(datum_len + 1);
strcpy(thermodynamic_params_path, datum);
thermodynamic_path_changed = 1;
}
/* check if path changes */
else if (strcmp(thermodynamic_params_path, datum)) {
free(thermodynamic_params_path);
thermodynamic_params_path = (char*) _rb_safe_malloc(datum_len + 1);
strcpy(thermodynamic_params_path, datum);
thermodynamic_path_changed = 1;
}
continue;
}
/* weights for objective functions */
/* CHANGE TEMP/temp -> TM/tm */
COMPARE_FLOAT("PRIMER_WT_TM_GT", pa->p_args.weights.temp_gt);
COMPARE_FLOAT("PRIMER_WT_TM_LT", pa->p_args.weights.temp_lt);
COMPARE_FLOAT("PRIMER_WT_GC_PERCENT_GT", pa->p_args.weights.gc_content_gt);
COMPARE_FLOAT("PRIMER_WT_GC_PERCENT_LT", pa->p_args.weights.gc_content_lt);
COMPARE_FLOAT("PRIMER_WT_SIZE_LT", pa->p_args.weights.length_lt);
COMPARE_FLOAT("PRIMER_WT_SIZE_GT", pa->p_args.weights.length_gt);
COMPARE_FLOAT("PRIMER_WT_SELF_ANY", pa->p_args.weights.compl_any);
COMPARE_FLOAT("PRIMER_WT_SELF_END", pa->p_args.weights.compl_end);
COMPARE_FLOAT("PRIMER_WT_SELF_ANY_TH", pa->p_args.weights.compl_any_th);
COMPARE_FLOAT("PRIMER_WT_SELF_END_TH", pa->p_args.weights.compl_end_th);
COMPARE_FLOAT("PRIMER_WT_HAIRPIN_TH", pa->p_args.weights.hairpin_th);
COMPARE_FLOAT("PRIMER_WT_NUM_NS", pa->p_args.weights.num_ns);
COMPARE_FLOAT("PRIMER_WT_LIBRARY_MISPRIMING", pa->p_args.weights.repeat_sim);
COMPARE_FLOAT("PRIMER_WT_SEQ_QUAL", pa->p_args.weights.seq_quality);
COMPARE_FLOAT("PRIMER_WT_END_QUAL", pa->p_args.weights.end_quality);
COMPARE_FLOAT("PRIMER_WT_POS_PENALTY", pa->p_args.weights.pos_penalty);
COMPARE_FLOAT("PRIMER_WT_END_STABILITY",
pa->p_args.weights.end_stability);
COMPARE_FLOAT("PRIMER_WT_TEMPLATE_MISPRIMING",
pa->p_args.weights.template_mispriming);
COMPARE_FLOAT("PRIMER_WT_TEMPLATE_MISPRIMING_TH",
pa->p_args.weights.template_mispriming_th);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_TM_GT", pa->o_args.weights.temp_gt);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_TM_LT", pa->o_args.weights.temp_lt);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_GC_PERCENT_GT", pa->o_args.weights.gc_content_gt);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_GC_PERCENT_LT", pa->o_args.weights.gc_content_lt);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SIZE_LT", pa->o_args.weights.length_lt);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SIZE_GT", pa->o_args.weights.length_gt);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SELF_ANY", pa->o_args.weights.compl_any);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SELF_END", pa->o_args.weights.compl_end);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SELF_ANY_TH", pa->o_args.weights.compl_any_th);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SELF_END_TH", pa->o_args.weights.compl_end_th);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_HAIRPIN_TH", pa->o_args.weights.hairpin_th);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_NUM_NS", pa->o_args.weights.num_ns);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_LIBRARY_MISHYB", pa->o_args.weights.repeat_sim);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_SEQ_QUAL", pa->o_args.weights.seq_quality);
COMPARE_FLOAT("PRIMER_INTERNAL_WT_END_QUAL", pa->o_args.weights.end_quality);
COMPARE_FLOAT("PRIMER_WT_TEMPLATE_MISPRIMING_TH",
pa->o_args.weights.template_mispriming_th);
COMPARE_FLOAT("PRIMER_PAIR_WT_PR_PENALTY",
pa->pr_pair_weights.primer_quality);
COMPARE_FLOAT("PRIMER_PAIR_WT_IO_PENALTY",
pa->pr_pair_weights.io_quality);
COMPARE_FLOAT("PRIMER_PAIR_WT_DIFF_TM",
pa->pr_pair_weights.diff_tm);
COMPARE_FLOAT("PRIMER_PAIR_WT_COMPL_ANY",
pa->pr_pair_weights.compl_any);
COMPARE_FLOAT("PRIMER_PAIR_WT_COMPL_END",
pa->pr_pair_weights.compl_end);
COMPARE_FLOAT("PRIMER_PAIR_WT_COMPL_ANY_TH",
pa->pr_pair_weights.compl_any_th);
COMPARE_FLOAT("PRIMER_PAIR_WT_COMPL_END_TH",
pa->pr_pair_weights.compl_end_th);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_TM_LT",
pa->pr_pair_weights.product_tm_lt);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_TM_GT",
pa->pr_pair_weights.product_tm_gt);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_SIZE_GT",
pa->pr_pair_weights.product_size_gt);
COMPARE_FLOAT("PRIMER_PAIR_WT_PRODUCT_SIZE_LT",
pa->pr_pair_weights.product_size_lt);
COMPARE_FLOAT("PRIMER_PAIR_WT_LIBRARY_MISPRIMING",
pa->pr_pair_weights.repeat_sim);
COMPARE_FLOAT("PRIMER_PAIR_WT_TEMPLATE_MISPRIMING",
pa->pr_pair_weights.template_mispriming);
COMPARE_FLOAT("PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH",
pa->pr_pair_weights.template_mispriming_th);
}
/* End of reading the tags in the right place */
/* Complain about unrecognized tags */
if (*strict_tags == 1) {
pr_append_new_chunk(glob_err, "Unrecognized tag: ");
pr_append(glob_err, s);
fprintf(stderr, "Unrecognized tag: %s\n", s);
}
} /* while ((s = p3_read_line(stdin)) != NULL && strcmp(s,"=")) { */
/* Check if the record was terminated by "=" */
if (NULL == s) { /* End of file. */
if (data_found) {
pr_append_new_chunk(glob_err,
"Final record not terminated by '='");
return 1;
} else return 0;
}
/* Figure out the right settings for the tasks*/
if (task_tmp != NULL) {
if (!strcmp_nocase(task_tmp, "pick_pcr_primers")) {
pa->primer_task = generic;
pa->pick_left_primer = 1;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 0;
} else if (!strcmp_nocase(task_tmp, "pick_pcr_primers_and_hyb_probe")) {
pa->primer_task = generic;
pa->pick_left_primer = 1;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 1;
} else if (!strcmp_nocase(task_tmp, "pick_left_only")) {
pa->primer_task = generic;
pa->pick_left_primer = 1;
pa->pick_right_primer = 0;
pa->pick_internal_oligo = 0;
} else if (!strcmp_nocase(task_tmp, "pick_right_only")) {
pa->primer_task = generic;
pa->pick_left_primer = 0;
pa->pick_right_primer = 1;
pa->pick_internal_oligo = 0;
} else if (!strcmp_nocase(task_tmp, "pick_hyb_probe_only")) {
pa->primer_task = generic;
pa->pick_left_primer = 0;
pa->pick_right_primer = 0;
pa->pick_internal_oligo = 1;
} else if (!strcmp_nocase(task_tmp, "generic")) {
pa->primer_task = generic;
} else if (!strcmp_nocase(task_tmp, "pick_detection_primers")) {
pa->primer_task = generic; /* Deliberate duplication for
backward compatibility. */
} else if (!strcmp_nocase(task_tmp, "pick_cloning_primers")) {
pa->primer_task = pick_cloning_primers;
} else if (!strcmp_nocase(task_tmp, "pick_discriminative_primers")) {
pa->primer_task = pick_discriminative_primers;
} else if (!strcmp_nocase(task_tmp, "pick_sequencing_primers")) {
pa->primer_task = pick_sequencing_primers;
} else if (!strcmp_nocase(task_tmp, "pick_primer_list")) {
pa->primer_task = pick_primer_list;
} else if (!strcmp_nocase(task_tmp, "check_primers")) {
pa->primer_task = check_primers;
/* check_primers sets the picking flags itself */
pa->pick_left_primer = 0;
pa->pick_right_primer = 0;
pa->pick_internal_oligo = 0;
if (sa->left_input){
pa->pick_left_primer = 1;
}
if (sa->right_input){
pa->pick_right_primer = 1;
}
if (sa->internal_input){
pa->pick_internal_oligo = 1;
}
} else
pr_append_new_chunk(glob_err,
"Unrecognized PRIMER_TASK");
free(task_tmp);
}
/*
* WARNING: read_and_create_seq_lib uses p3_read_line, so repeat
* library files cannot be read inside the
* while ((s = p3_read_line(stdin))...) loop above.
*
* FIX ME, in fact the reading
* of the library contents probably belongs inside
* primer3_boulder_main.c or libprimer3.c.
*/
/* Read in the repeat libraries */
if (NULL != repeat_file_path) {
destroy_seq_lib(pa->p_args.repeat_lib);
if ('\0' == *repeat_file_path) {
/* Input now specifies no repeat library. */
pa->p_args.repeat_lib = NULL;
}
else {
pa->p_args.repeat_lib
= read_and_create_seq_lib(repeat_file_path,
"mispriming library");
if(pa->p_args.repeat_lib->error.data != NULL) {
pr_append_new_chunk(glob_err, pa->p_args.repeat_lib->error.data);
}
}
free(repeat_file_path);
repeat_file_path = NULL;
}
/* Read in the repeat libraries for internal oligo */
if (NULL != int_repeat_file_path) {
destroy_seq_lib(pa->o_args.repeat_lib);
if ('\0' == *int_repeat_file_path) {
/* Input now specifies no mishybridization library. */
pa->o_args.repeat_lib = NULL;
}
else {
pa->o_args.repeat_lib =
read_and_create_seq_lib(int_repeat_file_path,
"internal oligo mishyb library");
if(pa->o_args.repeat_lib->error.data != NULL) {
pr_append_new_chunk(glob_err, pa->o_args.repeat_lib->error.data);
}
}
free(int_repeat_file_path);
int_repeat_file_path = NULL;
}
if (pa->primer_task == pick_pcr_primers_and_hyb_probe) {
PR_ASSERT(pa->pick_internal_oligo);
}
/* Removed 10/20/2010 as excessively compulsive, especially in the context
of taking input from web pages.
if ((min_3_prime || min_5_prime) && (sa->primer_overlap_junctions_count == 0)) {
pr_append_new_chunk(warnings,
"SEQUENCE_OVERLAP_JUNCTION_LIST not given, but "
"PRIMER_MIN_3_PRIME_OVERLAP_OF_JUNCTION or "
"PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION specified");
} */
return 1;
}
