first trial for a fasta formater

python/obitools3/format/fasta.pxd

@@ -6,4 +6,4 @@ cdef class FastaFormat:
     cdef HeaderFormat headerFormater
     
     cdef size_t  sequenceBufferLength
-    cdef cvarray sequenceBuffer
+    cdef char*   sequenceBuffer

python/obitools3/format/fasta.pyx

@@ -1,4 +1,6 @@
 cimport cython
+from libc.stdlib cimport malloc, free, realloc
+from libc.string cimport strncpy
 
 cdef class FastaFormat:
 	
@@ -7,32 +9,30 @@ cdef class FastaFormat:
 										   tags,
 										   printNAKeys)
 
+
+	def __cinit(self):
 		self.sequenceBufferLength=1000
-		self.sequenceBuffer = cvarray(shape=(1000,),
+		self.sequenceBuffer = malloc(self.sequenceBufferLength)
-									  itemsize=sizeof(char), 
+		
-									  format="c",
+	def __dealloc__(self)
-									  mode="c",
+		free(self.sequenceBuffer)
-									  allocate_buffer=True)
+		
 	@cython.boundscheck(False)	
 	def __call__(self, dict data):
 		cdef bytes brawseq      = <bytes> data['sequence']
+		cdef char* crowseq      = <char*> brawseq
 		cdef size_t lseq        = len(brawseq)
 		cdef size_t needed_size = lseq + 1
-		cdef char[:] seq
-		cdef char[:] fasta
 		cdef size_t k=0
+
 		needed_size += needed_size/ 50
 		
 		if needed_size > self.sequenceBufferLength:
 			self.sequenceBufferLength=needed_size
-			self.sequenceBuffer = cvarray(shape=(needed_size,),
+			self.sequenceBuffer = realloc(self.sequenceBuffer,
-										  itemsize=sizeof(char), 
+										  self.sequenceBufferLength
-										  format="c",
+										 )
-										  mode="c",
-										  allocate_buffer=True)
 			
-		seq   = brawseq
-		fasta = self.sequenceBuffer
 		
 		for i in range(0,lseq,60):
 			if i+60 <= lseq: