Start of the implementation of the export methods

python/obitools3/format/fasta.pxd

@@ -0,0 +1,9 @@
+from .header cimport HeaderFormat
+from cython.view cimport array as cvarray
+
+cdef class FastaFormat:
+
+    cdef HeaderFormat headerFormater
+    
+    cdef size_t  sequenceBufferLength
+    cdef cvarray sequenceBuffer

python/obitools3/format/fasta.pyx

@@ -0,0 +1,52 @@
+cimport cython
+
+cdef class FastaFormat:
+	
+	def __init__(self, list tags=[], bint printNAKeys=False):
+		self.headerFormater = HeaderFormat(True,
+										   tags,
+										   printNAKeys)
+
+		self.sequenceBufferLength=1000
+		self.sequenceBuffer = cvarray(shape=(1000,),
+									  itemsize=sizeof(char), 
+									  format="c",
+									  mode="c",
+									  allocate_buffer=True)
+	@cython.boundscheck(False)	
+	def __call__(self, dict data):
+		cdef bytes brawseq      = <bytes> data['sequence']
+		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,),
+										  itemsize=sizeof(char), 
+										  format="c",
+										  mode="c",
+										  allocate_buffer=True)
+			
+		seq   = brawseq
+		fasta = self.sequenceBuffer
+		
+		for i in range(0,lseq,60):
+			if i+60 <= lseq:
+				fasta[k:(k+60)]=seq[i:(i+60)]
+				fasta[k+60]='\n'
+				k+=61
+			else:
+				fasta[k:(k+lseq-i)]=seq[i:lseq]
+				k+=lseq-i
+				
+		
+				
+			
+		
+		
+		
+		

python/obitools3/format/header.pxd

@@ -0,0 +1,5 @@
+cdef class HeaderFormat:
+
+    cdef str    start
+    cdef size_t headerBufferLength
+    

python/obitools3/format/header.pyx

@@ -0,0 +1,27 @@
+
+cdef class HeaderFormat:
+    
+    def __init__(self, bint fastaHeader=True, list tags=[], bint printNAKeys=False):
+        
+        self.tags           = tags 
+        self.printNaKeys    = printNAKeys
+        
+        if fastaHeader:
+            self.start=">"
+        else:
+            self.start="@"
+        
+        self.headerBufferLength = 1000
+        self.headerBuffer = []
+        
+    def __call__(self, dict data):
+        cdef str header
+        
+        if data['definition'] is not None:
+            header = "%s%s %s" % (self.start,data['id'],
+                                  data['definition'])
+        else:
+            header = "%s%s" % (self.start,data['id'])
+            
+        return header
+