bool binspector_parser_t::is_named_statement()
{
return is_invariant() ||
is_constant() ||
is_skip() ||
is_slot() ||
is_signal() ||
is_field(); // field should be last because atoms only
// require an expression which most everything
// falls into; the more explicit stuff should
// come first.
}
/* given a list of 5' and 3' splice sites extracted from a group,
check whether they form valid pairs in all species */
int are_introns_okay(List *intron_splice, MSA *msa, List *problems,
int offset5, int offset3) {
int i, j, start1, start2;
char str1[3], str2[3], str12[5];
char strand;
int retval = 1;
char * splice_pairs[3] = {"GTAG", "GCAG", "ATAC"};
str1[2] = '\0'; str2[2] = '\0';
if (lst_size(intron_splice) < 2) return 1;
strand = ((GFF_Feature*)lst_get_ptr(intron_splice, 0))->strand;
/* assume all same strand */
if (strand == '+')
lst_qsort(intron_splice, feature_comparator_ascending);
else
lst_qsort(intron_splice, feature_comparator_descending);
for (i = 0; i < lst_size(intron_splice) - 1; i++) {
/* assume every 5' splice and immediately following 3' splice
form a pair */
GFF_Feature *f1 = lst_get_ptr(intron_splice, i);
GFF_Feature *f2 = lst_get_ptr(intron_splice, i+1);
if (str_starts_with_charstr(f1->feature, SPLICE_5) &&
str_starts_with_charstr(f2->feature, SPLICE_3)) {
start1 = f1->start - 1 + (strand == '-' ? offset5 : 0);
start2 = f2->start - 1 + (strand == '+' ? offset3 : 0);
for (j = 0; j < msa->nseqs; j++) {
str1[0] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start1], j, 0);
str1[1] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start1+1], j, 0);
str2[0] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start2], j, 0);
str2[1] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start2+1], j, 0);
if (strand == '-') {
msa_reverse_compl_seq(str1, 2);
msa_reverse_compl_seq(str2, 2);
}
strcpy(str12, str1); strcat(str12, str2);
if (!is_signal(str12, 3, splice_pairs, msa->is_missing)) {
problem_add(problems, f1, BAD_INTRON, -1, -1);
problem_add(problems, f2, BAD_INTRON, -1, -1);
retval = 0;
break;
}
}
i++; /* no need to look at next feature */
}
}
return retval;
}
static PHAST_INLINE
int is_conserved_stop(GFF_Feature *feat, MSA *msa) {
char tuplestr[4];
int j;
int start = feat->start - 1;
tuplestr[3] = '\0';
char * stop_signals[3] = { "TAA", "TAG", "TGA" };
for (j = 0; j < msa->nseqs; j++) {
tuplestr[0] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start], j, 0);
tuplestr[1] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start+1], j, 0);
tuplestr[2] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start+2], j, 0);
if (feat->strand == '-') msa_reverse_compl_seq(tuplestr, 3);
if (!is_signal(tuplestr, 3, stop_signals, msa->is_missing)) return 0;
}
return 1;
}
static PHAST_INLINE
int is_conserved_3splice(GFF_Feature *feat, MSA *msa, int offset3,
int splice_strict) {
char tuplestr[3];
int j, start = feat->start - 1; /* base 0 indexing */
if (feat->strand == '+') start += offset3;
tuplestr[2] = '\0';
char * splice_signals[2] = {"AG", "AC"};
for (j = 0; j < msa->nseqs; j++) {
tuplestr[0] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start], j, 0);
tuplestr[1] = ss_get_char_tuple(msa, msa->ss->tuple_idx[start+1], j, 0);
if (feat->strand == '-') msa_reverse_compl_seq(tuplestr, 2);
if (!is_signal(tuplestr, (splice_strict?1:2), splice_signals, msa->is_missing))
return 0;
}
return 1;
}
// Return 'true' if current entry is signal
bool NameList::current_is_signal() {
const char *entry = current();
return is_signal(entry);
}
