Cython: Added fasta and fastq writers

python/obitools3/writers/fasta.pxd

@@ -0,0 +1,9 @@
+#cython: language_level=3
+
+cdef class FastaNucWriter:
+    cdef object formatter
+    cdef object output
+    cdef int    only
+    cdef int    skip
+    cdef int    skipped
+    cdef int    read

python/obitools3/writers/fasta.pyx

@@ -0,0 +1,37 @@
+#cython: language_level=3
+
+'''
+Created on oct 12th 2018
+
+@author: celine.mercier.bioinfo@gmail.com
+'''
+
+    
+cdef class FastaNucWriter:
+    
+    def __init__(self, 
+                 object formatter, 
+                 object output_object, 
+                 int skip=0,
+                 only=None):
+                        
+        if only is None:
+            self.only = -1
+        else:
+            self.only = int(only)
+
+        self.formatter = formatter
+        self.output = output_object
+        self.skip = skip
+        self.skipped = 0
+        self.read = 0
+    
+    def __call__(self, object seq):
+        if self.only > -1 and self.read == self.only:
+            raise StopIteration
+        if self.skip > 0 and self.skipped < self.skip:
+            self.skipped += 1
+            return
+        self.output.write(self.formatter(seq))
+        self.output.write(b"\n")  # TODO is that clean?
+        self.read += 1

python/obitools3/writers/fastq.pxd

@@ -0,0 +1,9 @@
+#cython: language_level=3
+
+cdef class FastqWriter:
+    cdef object formatter
+    cdef object output
+    cdef int    only
+    cdef int    skip
+    cdef int    skipped
+    cdef int    read

python/obitools3/writers/fastq.pyx

@@ -0,0 +1,41 @@
+#cython: language_level=3
+
+'''
+Created on oct 14th 2018
+
+@author: celine.mercier.bioinfo@gmail.com
+'''
+
+    
+cdef class FastqWriter:
+    
+    def __init__(self, 
+                 object formatter, 
+                 object output_object, 
+                 int skip=0,
+                 only=None):
+        
+        self.formatter = formatter
+        self.output = output_object
+    
+        if only is None:
+            self.only = -1
+        else:
+            self.only = int(only)
+
+        self.formatter = formatter
+        self.output = output_object
+        self.skip = skip
+        self.skipped = 0
+        self.read = 0
+    
+    
+    def __call__(self, object seq):
+        if self.only > -1 and self.read == self.only:
+            raise StopIteration
+        if self.skip > 0 and self.skipped < self.skip:
+            self.skipped += 1
+            return
+        self.output.write(self.formatter(seq))
+        self.output.write(b"\n")  # TODO is that clean?
+        self.read += 1