Cython: fasta and fastq header formatter

python/obitools3/format/header.pxd

@@ -1,6 +1,6 @@
 cdef class HeaderFormat:
 
-    cdef str    start
+    cdef bytes  start
     cdef set    tags
     cdef bint   printNaKeys
     cdef size_t headerBufferLength

python/obitools3/format/header.pyx

@@ -1,11 +1,22 @@
+#cython: language_level=3
+
+from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
+                                        ID_COLUMN, \
+                                        DEFINITION_COLUMN, \
+                                        QUALITY_COLUMN, \
+                                        COUNT_COLUMN
+
+from obitools3.utils cimport str2bytes
+
 
 cdef class HeaderFormat:
     
-    def __init__(self, bint fastaHeader=True, list tags=[], bint printNAKeys=False):
+    SPECIAL_KEYS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
+    
+    def __init__(self, str format="fasta", list tags=[], bint printNAKeys=False):
         '''
-        
+            @param format: 
-            @param fastaHeader: 
+            @type  format: `str`
-            @type  fastaHeader: `bool`
             
             @param tags:
             @type  tags: `list` of `bytes`
@@ -17,44 +28,42 @@ cdef class HeaderFormat:
         self.tags           = set(tags)
         self.printNaKeys    = printNAKeys
         
-        if fastaHeader:
+        if format=="fasta":
-            self.start=">"
+            self.start=b">"
-        else:
+        elif format=="fastq":
-            self.start="@"
+            self.start=b"@"
         
         self.headerBufferLength = 1000
-        #self.headerBuffer = []
+
         
-    def __call__(self, dict data):
+    def __call__(self, object data):
-        cdef str header
+        cdef bytes header
-        cdef dict tags = data['tags']
+        cdef list tags = [key for key in data if key not in self.SPECIAL_KEYS]
         cdef set  ktags
-        cdef list lines = [""]
+        cdef list lines = [b""]
-        cdef str tagline
+        cdef bytes tagline
+        
         
         if self.tags is not None and self.tags:
             ktags = self.tags
         else:
-            ktags = set(tags.keys())
+            ktags = set(tags)
             
         for k in ktags:
             if k in tags:
-                value = tags[k]
+                value = data[k]
                 if value is not None or self.printNaKeys:
-                    lines.append("%s=%s;" % (k,tags[k]))
+                    lines.append(k + b"=" + str2bytes(str(data[k])))   #TODO bytes() method on values (str equivalent)
                     
         if len(lines) > 1:
-            tagline=" ".join(lines)
+            tagline=b" ".join(lines)
         else:
-            tagline=""
+            tagline=b""
             
-        if data['definition'] is not None:
+        if data[DEFINITION_COLUMN] is not None:
-            header = "%s%s%s %s" % (self.start,data['id'],
+            header = self.start + data[ID_COLUMN] + tagline + b" " + data[DEFINITION_COLUMN]
-                                    tagline,
-                                    data['definition'])
         else:
-            header = "%s%s%s" % (self.start,data['id'],
+            header = self.start + data[ID_COLUMN] + tagline
-                                 tagline)
+             
-            
         return header