update

Author: lmdu

.github/workflows/wheel.yml

@@ -52,6 +52,8 @@ jobs:
         with:
           python-version: "3.12"
 
+      - run: pip install setuptools
+
       - name: Build sdist
         run: python setup.py sdist
 

src/fasta.c

@@ -121,6 +121,7 @@ PyObject *pyfastx_fasta_new(PyTypeObject *type, PyObject *args, PyObject *kwargs
 		PYFASTX_SQLITE_CALL(
 			sqlite3_prepare_v2(obj->index->index_db, "SELECT * FROM seq WHERE chrom=? LIMIT 1;", -1, &obj->index->seq_stmt, NULL);
 			sqlite3_prepare_v2(obj->index->index_db, "SELECT * FROM seq WHERE ID=? LIMIT 1;", -1, &obj->index->uid_stmt, NULL);
+			sqlite3_prepare_v2(obj->index->index_db, "SELECT * FROM comp WHERE ID=? LIMIT 1;", -1, &obj->index->comp_stmt, NULL);
 		);
 	}
 
@@ -1060,7 +1061,6 @@ PyObject *pyfastx_fasta_gc_skew(pyfastx_Fasta *self, void* closure) {
 }
 
 PyObject *pyfastx_fasta_composition(pyfastx_Fasta *self, void* closure) {
-	int i;
 	int l;
 	int ret;
 	const char *sql;

src/index.c

@@ -84,6 +84,7 @@ pyfastx_Index* pyfastx_init_index(PyObject *obj, PyObject* file_obj, PyObject* i
 	index->iter_stmt = NULL;
 	index->uid_stmt = NULL;
 	index->seq_stmt = NULL;
+	index->comp_stmt = NULL;
 
 	//cache sequence
 	//index->cache_name = {0,0,0};
@@ -445,6 +446,10 @@ void pyfastx_index_free(pyfastx_Index *self){
 		PYFASTX_SQLITE_CALL(sqlite3_finalize(self->seq_stmt));
 	}
 
+	if (self->comp_stmt) {
+		PYFASTX_SQLITE_CALL(sqlite3_finalize(self->comp_stmt));
+	}
+
 	if (self->index_db) {
 		PYFASTX_SQLITE_CALL(sqlite3_close(self->index_db));
 		self->index_db = NULL;

src/index.h

@@ -65,6 +65,7 @@ typedef struct {
 	sqlite3_stmt *iter_stmt;
 	sqlite3_stmt *uid_stmt;
 	sqlite3_stmt *seq_stmt;
+	sqlite3_stmt *comp_stmt;
 
 	//parent fasta object
 	PyObject *fasta;

src/sequence.c

@@ -564,25 +564,20 @@ PyObject *pyfastx_sequence_gc_content(pyfastx_Sequence *self, void* closure) {
 	int ret;
 	char *seq;
 
-	sqlite3_stmt *stmt;
-
 	Py_ssize_t i, n;
 	Py_ssize_t a = 0, c = 0, g = 0, t = 0;
-
-	const char *sql = "SELECT * FROM comp WHERE seqid=?";
 
 	PYFASTX_SQLITE_CALL(
-		sqlite3_prepare_v2(self->index->index_db, sql, -1, &stmt, NULL);
-		sqlite3_bind_int64(stmt, 1, self->id);
-		ret = sqlite3_step(stmt);
+		sqlite3_bind_int64(self->index->comp_stmt, 1, self->id);
+		ret = sqlite3_step(self->index->comp_stmt);
 	);
 
 	if (ret == SQLITE_ROW && self->start == 1 && self->end == self->seq_len) {
 		while (ret == SQLITE_ROW) {
 			PYFASTX_SQLITE_CALL(
-				l = sqlite3_column_int(stmt, 2);
-				n = sqlite3_column_int64(stmt, 3);
-				ret = sqlite3_step(stmt);
+				l = sqlite3_column_int(self->index->comp_stmt, 2);
+				n = sqlite3_column_int64(self->index->comp_stmt, 3);
+				ret = sqlite3_step(self->index->comp_stmt);
 			);
 
 			switch (l) {
@@ -635,7 +630,7 @@ PyObject *pyfastx_sequence_gc_content(pyfastx_Sequence *self, void* closure) {
 		}
 	}
 
-	PYFASTX_SQLITE_CALL(sqlite3_finalize(stmt));
+	PYFASTX_SQLITE_CALL(sqlite3_reset(self->index->comp_stmt));
 
 	return Py_BuildValue("f", (float)(g+c)/(a+c+g+t)*100);
 }
@@ -644,25 +639,21 @@ PyObject *pyfastx_sequence_gc_skew(pyfastx_Sequence *self, void* closure) {
 	int l;
 	int ret;
 	char *seq;
-	sqlite3_stmt *stmt;
 
 	Py_ssize_t i, n;
 	Py_ssize_t c = 0, g = 0;
-
-	const char *sql = "SELECT * FROM comp WHERE seqid=?";
 
 	PYFASTX_SQLITE_CALL(
-		sqlite3_prepare_v2(self->index->index_db, sql, -1, &stmt, NULL);
-		sqlite3_bind_int64(stmt, 1, self->id);
-		ret = sqlite3_step(stmt);
+		sqlite3_bind_int64(self->index->comp_stmt, 1, self->id);
+		ret = sqlite3_step(self->index->comp_stmt);
 	);
 
 	if (ret == SQLITE_ROW && self->start == 1 && self->end == self->seq_len) {
 		while (ret == SQLITE_ROW) {
 			PYFASTX_SQLITE_CALL(
-				l = sqlite3_column_int(stmt, 2);
-				n = sqlite3_column_int64(stmt, 3);
-				ret = sqlite3_step(stmt);
+				l = sqlite3_column_int(self->index->comp_stmt, 2);
+				n = sqlite3_column_int64(self->index->comp_stmt, 3);
+				ret = sqlite3_step(self->index->comp_stmt);
 			);
 
 			switch (l) {
@@ -695,7 +686,7 @@ PyObject *pyfastx_sequence_gc_skew(pyfastx_Sequence *self, void* closure) {
 		}
 	}
 
-	PYFASTX_SQLITE_CALL(sqlite3_finalize(stmt));
+	PYFASTX_SQLITE_CALL(sqlite3_reset(self->index->comp_stmt));
 
 	return Py_BuildValue("f", (float)(g-c)/(g+c));
 }
@@ -705,8 +696,6 @@ PyObject *pyfastx_sequence_composition(pyfastx_Sequence *self, void* closure) {
 	int l;
 	int ret;
 	char *seq;
-
-	sqlite3_stmt *stmt;
 
 	Py_ssize_t n;
 	Py_ssize_t seq_comp[128] = {0};
@@ -715,22 +704,19 @@ PyObject *pyfastx_sequence_composition(pyfastx_Sequence *self, void* closure) {
 	PyObject *b;
 	PyObject *c;
 
-	const char *sql = "SELECT * FROM comp WHERE ID=?";
-
 	PYFASTX_SQLITE_CALL(
-		sqlite3_prepare_v2(self->index->index_db, sql, -1, &stmt, NULL);
-		sqlite3_bind_int64(stmt, 1, self->id);
-		ret = sqlite3_step(stmt);
+		sqlite3_bind_int64(self->index->stmt, 1, self->id);
+		ret = sqlite3_step(self->index->stmt);
 	);
 
 	d = PyDict_New();
 
 	if (ret == SQLITE_ROW && self->start == 1 && self->end == self->seq_len) {
 		while (ret == SQLITE_ROW) {
 			PYFASTX_SQLITE_CALL(
-				l = sqlite3_column_int(stmt, 2);
-				n = sqlite3_column_int64(stmt, 3);
-				ret = sqlite3_step(stmt);
+				l = sqlite3_column_int(self->index->stmt, 2);
+				n = sqlite3_column_int64(self->index->stmt, 3);
+				ret = sqlite3_step(self->index->stmt);
 			);
 
 			if (n > 0 && l >= 32 && l < 127) {
@@ -761,8 +747,7 @@ PyObject *pyfastx_sequence_composition(pyfastx_Sequence *self, void* closure) {
 		}
 	}
 
-	PYFASTX_SQLITE_CALL(sqlite3_finalize(stmt));
-
+	PYFASTX_SQLITE_CALL(sqlite3_reset(self->index->stmt));
 	return d;
 }