Cython: fasta and fastq parsers now return bytes and take NA string

argument

python/obitools3/format/fasta.pyx

@@ -7,10 +7,11 @@ from obitools3.utils cimport bytes2str
 
 cdef class FastaFormat:
 	
-	def __init__(self, list tags=[], bint printNAKeys=False):
+	def __init__(self, list tags=[], bint printNAKeys=False, bytes NAString=b"NA"):
 		self.headerFormatter = HeaderFormat("fasta",
-										    tags,
-										    printNAKeys)
+										    tags=tags,
+										    printNAKeys=printNAKeys,
+										    NAString=NAString)
 		
 	@cython.boundscheck(False)	
 	def __call__(self, object data):
@@ -24,5 +25,5 @@ cdef class FastaFormat:
 			
 		brawseq = b'\n'.join(lines)
 		
-		return bytes2str(self.headerFormatter(data) + b"\n" + brawseq)
+		return self.headerFormatter(data) + b"\n" + brawseq
 					

python/obitools3/format/fastq.pyx

@@ -5,28 +5,25 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN
 from obitools3.utils cimport bytes2str, str2bytes, tobytes
 
 
-# TODO quality offset option
+# TODO quality offset option?
 cdef class FastqFormat:
 	
-	def __init__(self, list tags=[], bint printNAKeys=False):
+	def __init__(self, list tags=[], bint printNAKeys=False, bytes NAString=b"NA"):
 		self.headerFormatter = HeaderFormat("fastq",
-										    tags,
-										    printNAKeys)
+										    tags=tags,
+										    printNAKeys=printNAKeys,
+										    NAString=NAString)
 		
 	@cython.boundscheck(False)	
 	def __call__(self, object data):
 		
 		cdef bytes quality	
 		
-		if hasattr(data, "quality_str"):
-			quality = str2bytes(data.quality_str)    # TODO quality_bytes property
+		if hasattr(data, "quality_bytes"):
+			quality = data.quality_bytes
 		elif hasattr(data, "quality"):
 			quality = tobytes(data.quality)
 		else:
 			raise AttributeError("No quality when exporting to fastq")  # TODO discuss
 		
-		return bytes2str(self.headerFormatter(data) + 
-						b"\n" + 
-						data[NUC_SEQUENCE_COLUMN] +
-						b"\n+\n" + 
-						quality)   
+		return self.headerFormatter(data) + b"\n" + data[NUC_SEQUENCE_COLUMN] + b"\n+\n" + quality

python/obitools3/format/header.pxd

@@ -2,6 +2,7 @@ cdef class HeaderFormat:
 
     cdef bytes  start
     cdef set    tags
-    cdef bint   printNaKeys
+    cdef bint   printNAKeys
+    cdef bytes  NAString
     cdef size_t headerBufferLength
     

python/obitools3/format/header.pyx

@@ -7,13 +7,14 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                                         COUNT_COLUMN
 
 from obitools3.utils cimport str2bytes
+from obitools3.dms.column.column cimport Column_line
 
 
 cdef class HeaderFormat:
     
     SPECIAL_KEYS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
     
-    def __init__(self, str format="fasta", list tags=[], bint printNAKeys=False):
+    def __init__(self, str format="fasta", list tags=[], bint printNAKeys=False, bytes NAString=b"NA"):
         '''
             @param format: 
             @type  format: `str`
@@ -23,10 +24,14 @@ cdef class HeaderFormat:
             
             @param printNAKeys: 
             @type  printNAKeys: `bool` 
+            
+            @param NAString:
+            @type NAString: `bytes`
         '''
         
         self.tags           = set(tags)
-        self.printNaKeys    = printNAKeys
+        self.printNAKeys    = printNAKeys
+        self.NAString       = NAString
         
         if format=="fasta":
             self.start=b">"
@@ -43,7 +48,6 @@ cdef class HeaderFormat:
         cdef list lines = [b""]
         cdef bytes tagline
         
-        
         if self.tags is not None and self.tags:
             ktags = self.tags
         else:
@@ -52,8 +56,16 @@ cdef class HeaderFormat:
         for k in ktags:
             if k in tags:
                 value = data[k]
-                if value is not None or self.printNaKeys:
-                    lines.append(k + b"=" + str2bytes(str(data[k])))   #TODO bytes() method on values (str equivalent)
+                if value is None:
+                    if self.printNAKeys:
+                        value = self.NAString
+                else:
+                    if type(value) == Column_line:
+                        value = value.bytes()
+                    else:
+                        value = str2bytes(str(value))   # TODO ugly but how else?
+                if value is not None:
+                    lines.append(k + b"=" + value + b";")   
                 
         if len(lines) > 1:
             tagline=b" ".join(lines)