Add inital wrapperHEADmain

4 files changed, 200 insertions, 0 deletions

diff --git a/pyqidx/__init__.py b/pyqidx/__init__.py
new file mode 100644
index 0000000..3b515a1
--- /dev/null
+++ b/pyqidx/__init__.py
@@ -0,0 +1,5 @@
+from pyqidx.qidx import (
+	AlignmentRecord,
+	QidxException,
+	QueryIndexFile
+)
diff --git a/pyqidx/qidx.py b/pyqidx/qidx.py
new file mode 100644
index 0000000..95f5113
--- /dev/null
+++ b/pyqidx/qidx.py
@@ -0,0 +1,108 @@
+from pyqidx._qidx import ffi, lib
+
+from typing import (
+	NamedTuple,
+	Generator,
+	BinaryIO,
+	Union,
+	Optional
+)
+
+class _QidxError( object ):
+
+	code : int
+
+	def __init__( self, code : int ):
+		self.code = code
+
+	@staticmethod
+	def from_code( code ):
+		return _QidxError( code )
+
+	@property
+	def message( self ):
+		_msg = ffi.string( lib.qidx_strerr( self.code ) )
+		return str( _msg , encoding='UTF-8' )
+
+class QidxException( Exception ):
+	
+	@staticmethod
+	def from_code( err_code ):
+		return QidxException( _QidxError( err_code ).message )
+
+class AlignmentRecord( NamedTuple ):
+	tid : int
+	pos : int
+	vptr : int
+
+class _Qidx( object ):
+
+	def __init__( self, fd : int ):
+		self._qidx = ffi.new('qidx_fp_t **')
+
+		err = lib.qidx_open( self._qidx, fd )
+
+		if err != lib.QIDX_OK:
+			raise QidxException.from_code( err )
+
+	def lookup_alignments( self, query_name : str ) \
+		-> Generator[AlignmentRecord, None, None]:
+		qname = ffi.new("char[]", bytes( query_name, encoding="UTF-8" ))
+
+		rec = ffi.new('qidx_record_t **')
+		err = lib.qidx_lookup_alnrec(self._qidx[0], qname, rec)
+
+		if not rec[0]:
+			return
+
+		for i in range(rec[0].n_alns):
+			aln = rec[0].alns[i]
+			yield AlignmentRecord( aln.tid, aln.pos, aln.vptr )
+
+		lib.qidx_free_alnrec( rec[0] )
+
+	def close( self ):
+		err = lib.qidx_close( self._qidx[0] )
+
+		if err != lib.QIDX_OK:
+			raise QidxException.from_code( err )
+
+class QueryIndexFile( object ):
+
+	_filename : Optional[ str ]
+	_file : BinaryIO
+	_qidx : _Qidx
+
+	def __init__( self, filename_or_file : Union[ BinaryIO, str ] ):
+
+		if isinstance( filename_or_file, str ):
+			self._filename = filename_or_file
+			self._file = None
+		else:
+			self._file = filename_or_file
+			self._filename = None
+
+		self._qidx = None
+
+	def open( self ):
+		if self._filename:
+			self._file = open( self._filename, 'rb' )
+
+		self._qidx = _Qidx( self._file.fileno() )
+
+	def close( self ):
+		self._qidx.close()
+
+		if self._filename:
+			self._file.close()
+
+	def __enter__( self ):
+		self.open()
+		return self
+
+	def __exit__( self, exc_type, exc_value, tb ):
+		self.close()
+
+	def lookup_alignments( self, query_name : str ) \
+		-> Generator[AlignmentRecord, None, None]:
+		return (yield from self._qidx.lookup_alignments( query_name ))
diff --git a/pyqidx_build.py b/pyqidx_build.py
new file mode 100644
index 0000000..1bf8e58
--- /dev/null
+++ b/pyqidx_build.py
@@ -0,0 +1,69 @@
+from cffi import FFI
+ffibuilder = FFI()
+
+ffibuilder.cdef("""
+	// @abstract Structure representing an unique alignment and virtual file pointer
+	// @field tid   chromosome ID
+	// @field pos   0-based leftmost coordinate
+	// @field vptr  virtual pointer
+	typedef struct {
+		uint32_t tid;
+		uint32_t pos;
+		uint64_t vptr;
+	} aln_spec_t;
+
+	// @abstract Structure representing all alignments by queryname
+	// @field qname    queryname (name for the given read)
+	// @field n_alns   number of alignments
+	// @field alns     array with alignments structures
+	typedef struct {
+		char * qname;
+		uint16_t n_alns;
+		aln_spec_t * alns;
+	} qidx_record_t;
+
+	typedef enum {
+		QIDX_OK = 0,
+		QIDX_ITER_DONE,
+		QIDX_NO_MEM,
+		QIDX_NO_BAM_HDR,
+		QIDX_BAM_READ_FAILURE,
+		QIDX_REC_ITER_FAILURE,
+		QIDX_NOT_SORTED,
+		QIDX_BUCKET_MAX_SIZE_EXCEEDED,
+		QIDX_MAP_FAIL,
+		QIDX_IO_FAIL,
+		QIDX_FAILED_TO_OPEN_BAMFILE,
+		QIDX_FAILED_TO_OPEN_INDEX_FILE,
+		QIDX_INVALID_VERSION,
+		QIDX_INVALID_MAGIC,
+	} qidx_err_t;
+
+	bool qidx_errno(qidx_err_t err);
+
+	char const * qidx_strerr(qidx_err_t err);
+
+	struct qidx_fp;
+	typedef struct qidx_fp qidx_fp_t;
+
+	qidx_err_t qidx_open(qidx_fp_t ** fp, int fd);
+	qidx_err_t qidx_create(qidx_fp_t ** fp, int fd, uint32_t _n_buckets,
+			uint32_t max_bucket_size);
+	qidx_err_t qidx_lookup_alnrec(qidx_fp_t * fp,
+			char const * qname, qidx_record_t ** rec);
+	void qidx_free_alnrec(qidx_record_t * rec);
+	qidx_err_t qidx_close(qidx_fp_t * fp);
+""")
+
+ffibuilder.set_source(
+	"pyqidx._qidx",
+"""
+     #include <qidx.h>   // the C header of the library
+""",
+	libraries=['qidx'],
+	extra_link_args=['-Wl,-rpath=/usr/local/lib'],
+)   # library name, for the linker
+
+
+if __name__ == "__main__":
+    ffibuilder.compile(verbose=True)
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..d12a6d8
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,18 @@
+from setuptools import setup
+
+import pyqidx_build as pyqidx_build
+
+setup(
+	name='pyqidx',
+	version='0.0.1',
+	author='Flu0r1ne',
+	author_email='flu0r1ne@flu0r1ne.net',
+	description='Python bindings for qidx',
+	url='https://git.flu0r1ne.net',
+	license='MIT',
+	setup_requires=["cffi>=1.0.0"],
+	cffi_modules=["pyqidx_build.py:ffibuilder"],
+	install_requires=["cffi>=1.0.0"],
+	packages=['pyqidx'],
+	ext_modules=[pyqidx_build.ffibuilder.distutils_extension()],
+)