added reverse complement func

docs/source/api_reference.rst

@@ -26,15 +26,29 @@ pyfastx.version
 
 	:rtype: bool
 
+.. py:function:: pyfastx.reverse_complement(seq)
+
+	New in pyfastx 2.0.0
+
+	get reverse complement sequence of given DNA sequence
+
+	:param str seq: DNA sequence
+
+	:return: reverse complement sequence
+
+	:rtype: str
+
 pyfastx.Fasta
 -------------
 
-.. py:class:: pyfastx.Fasta(file_name, uppercase=True, build_index=True, full_index=False, full_name=False, memory_index=False, key_func=None)
+.. py:class:: pyfastx.Fasta(file_name, index_file=None, uppercase=True, build_index=True, full_index=False, full_name=False, memory_index=False, key_func=None)
 
 	Read and parse fasta files. Fasta can be used as dict or list, you can use index or sequence name to get a sequence object, e.g. ``fasta[0]``, ``fasta['seq1']``
 
 	:param str file_name: the file path of input FASTA file
 
+	:param str index_file: the index file of FASTA file, default using index file with extension of .fxi in the same directory of FASTA file, New in 2.0.0
+
 	:param bool uppercase: always output uppercase sequence, default: ``True``
 
 	:param bool build_index: build index for random access to FASTA sequence, default: ``True``. If build_index is False, iteration will return a tuple (name, seq); If build_index is True, iteration will return a sequence object.
@@ -264,11 +278,13 @@ pyfastx.Fastq
 
 New in ``pyfastx`` 0.4.0
 
-.. py:class:: pyfastx.Fastq(file_name, phred=0, build_index=True, full_index=False)
+.. py:class:: pyfastx.Fastq(file_name, index_file=None, phred=0, build_index=True, full_index=False)
 
 	Read and parse fastq file
 
-	:param str file_name: input fastq file path
+	:param str file_name: input FASTQ file path
+
+	:param str index_file: the index file of FASTQ file, default using the index file with extension of .fxi in the same directory of FASTQ file. New in 2.0.0
 
 	:param bool build_index: build index for random access to FASTQ reads, default: ``True``. If build_index is False, iteration will return a tuple (name, seq, qual); If build_index is True, iteration will return a read object
 

docs/source/changelog.rst

@@ -1,6 +1,19 @@
 Changelog
 =========
 
+Version 2.0.0 (2023-09-05)
+--------------------------
+
+- Added support for file name with wide char
+- Added support for specifying index file path
+- Added support for more characters in DNA sequence
+- Added reverse complement function for DNA conversion
+- Improved the performance of kseq library
+- Optimized gzip index importing and saving without temp file
+- Fixed segmentation fault when using sequence composition
+- Fixed memory leak in Fastq read quality integer
+- Fixed zlib download url broken error when building
+
 Version 1.1.0 (2023-04-19)
 --------------------------
 
@@ -33,35 +46,38 @@ Version 0.9.0 (2022-12-30)
 - Fixed the quality score parsing error from fastq
 - Fixed the reference of sequence returned from function
 
+Older versions
+--------------
+
 Version 0.8.4 (2021-06-30)
---------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Added slice feature to FastaKeys
 - Fixed FastaKeys and FastqKeys iteration memory leak
 - Optimized FastaKeys and FastqKeys creation
 
 Version 0.8.3 (2021-04-25)
---------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Fixed Fastx iteration for next function
 - Fixed Fastx uppercase for reading fasta
 
 Version 0.8.2 (2021-01-02)
---------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Fixed sample segfault error caused by fastq iteration error
 - Fixed gzip index import error in multiple processes
 - Fixed fastq iteration segfault error with full_name=True
 - Fixed all objects iteration to support built-in next function
 
 Version 0.8.1 (2020-12-16)
---------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Fixed pip install error from source code
 - Removed support for python39 32bit due to dll load error
 
 Version 0.8.0 (2020-12-15)
---------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Added Fastx object as a simple sequence iterator
 - Added FastqKeys object to obtain read names
@@ -72,7 +88,7 @@ Version 0.8.0 (2020-12-15)
 - Changed Identifier object to FastaKeys object
 
 Version 0.7.0 (2020-09-20)
---------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 - Added support for extracting flank sequences
 - Added support for indexing super large gzip file
@@ -81,9 +97,6 @@ Version 0.7.0 (2020-09-20)
 - Fixed sequence dealloc error cuasing no fasta delloc trigger
 - Fixed fastq max and min quality score return value
 
-Older versions
---------------
-
 Version 0.6.17 (2020-08-31)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

src/index.c

@@ -584,7 +584,7 @@ PyObject *pyfastx_index_get_seq_by_id(pyfastx_Index *self, Py_ssize_t chrom){
 		);
 
 		return (PyObject *)obj;
-	} else { 
+	} else {
 		PYFASTX_SQLITE_CALL(sqlite3_reset(self->uid_stmt));
 		PyErr_SetString(PyExc_IndexError, "Index Error");
 		return NULL;

src/module.c

@@ -41,9 +41,27 @@ PyObject *pyfastx_gzip_check(PyObject *self, PyObject *args) {
 	Py_RETURN_FALSE;
 }
 
+PyObject *pyfastx_reverse_complement(PyObject *self, PyObject *args) {
+	const char *s;
+
+	PyObject *seq_obj;
+	PyObject *rc_obj;
+
+	if (!PyArg_ParseTuple(args, "O", &seq_obj)) {
+		return NULL;
+	}
+
+	s = PyUnicode_AsUTF8(seq_obj);
+	rc_obj = PyUnicode_FromString(s);
+	s = PyUnicode_AsUTF8(rc_obj);
+	reverse_complement_seq(s);
+	return rc_obj;
+}
+
 static PyMethodDef module_methods[] = {
 	{"version", (PyCFunction)pyfastx_version, METH_VARARGS | METH_KEYWORDS, NULL},
 	{"gzip_check", (PyCFunction)pyfastx_gzip_check, METH_VARARGS, NULL},
+	{"reverse_complement", (PyCFunction)pyfastx_reverse_complement, METH_VARARGS, NULL},
 	{NULL, NULL, 0, NULL}
 };
 

src/version.h

@@ -1,2 +1,2 @@
-#define PYFASTX_VERSION "1.2.0"
+#define PYFASTX_VERSION "2.0.0"
 #define ZRAN_VERSION "1.7.0"