From e39c1a7fbfd36304b8432d3a3f7d5d46e206fe9e Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Sun, 31 Mar 2019 15:38:34 +0200
Subject: [PATCH] Cython: added tab formatter and parser (for obi export)

---
 python/obitools3/format/tab.pxd  |  8 ++++++
 python/obitools3/format/tab.pyx  | 44 ++++++++++++++++++++++++++++++++
 python/obitools3/writers/tab.pxd |  9 +++++++
 python/obitools3/writers/tab.pyx | 43 +++++++++++++++++++++++++++++++
 4 files changed, 104 insertions(+)
 create mode 100755 python/obitools3/format/tab.pxd
 create mode 100755 python/obitools3/format/tab.pyx
 create mode 100755 python/obitools3/writers/tab.pxd
 create mode 100755 python/obitools3/writers/tab.pyx

diff --git a/python/obitools3/format/tab.pxd b/python/obitools3/format/tab.pxd
new file mode 100755
index 0000000..a434faa
--- /dev/null
+++ b/python/obitools3/format/tab.pxd
@@ -0,0 +1,8 @@
+#cython: language_level=3
+
+cdef class TabFormat:
+    cdef bint header
+    cdef bint first_line
+    cdef bytes NAString
+    cdef list tags
+    cdef bytes sep
\ No newline at end of file
diff --git a/python/obitools3/format/tab.pyx b/python/obitools3/format/tab.pyx
new file mode 100755
index 0000000..052b2bd
--- /dev/null
+++ b/python/obitools3/format/tab.pyx
@@ -0,0 +1,44 @@
+#cython: language_level=3
+
+cimport cython
+from obitools3.dms.view.view cimport Line
+from obitools3.utils cimport bytes2str_object, str2bytes, tobytes
+from obitools3.dms.column.column cimport Column_line
+
+
+cdef class TabFormat:
+    
+    def __init__(self, header=True, bytes NAString=b"NA", bytes sep=b"\t"):
+        self.header = True
+        self.first_line = True
+        self.NAString = NAString
+        self.sep = sep
+        
+    @cython.boundscheck(False)    
+    def __call__(self, object data):
+        
+        line = []
+        
+        if self.first_line:
+            self.tags = [k for k in data.keys()]
+        
+        for k in self.tags:
+            
+            if self.header and self.first_line:
+                value = tobytes(k)
+            else:
+                value = data[k]
+                if value is not None:
+                    if type(value) == Column_line:
+                        value = value.bytes()
+                    else:
+                        value = str2bytes(str(bytes2str_object(value))) # genius programming
+                if value is None:
+                    value = self.NAString
+            
+            line.append(value)   
+      	
+        if self.first_line:
+            self.first_line = False
+      		
+        return self.sep.join(value for value in line)
diff --git a/python/obitools3/writers/tab.pxd b/python/obitools3/writers/tab.pxd
new file mode 100755
index 0000000..0891c64
--- /dev/null
+++ b/python/obitools3/writers/tab.pxd
@@ -0,0 +1,9 @@
+#cython: language_level=3
+
+cdef class TabWriter:
+    cdef object formatter
+    cdef object output
+    cdef int    only
+    cdef int    skip
+    cdef int    skipped
+    cdef int    read
\ No newline at end of file
diff --git a/python/obitools3/writers/tab.pyx b/python/obitools3/writers/tab.pyx
new file mode 100755
index 0000000..f644910
--- /dev/null
+++ b/python/obitools3/writers/tab.pyx
@@ -0,0 +1,43 @@
+#cython: language_level=3
+
+'''
+Created on oct 12th 2018
+
+@author: celine.mercier.bioinfo@gmail.com
+'''
+
+    
+cdef class TabWriter:
+    
+    def __init__(self, 
+                 object formatter, 
+                 object output_object, 
+                 int skip=0,
+                 only=None,
+                 header=True):
+                        
+        if only is None:
+            self.only = -1
+        else:
+            self.only = int(only)
+            if header:
+                self.only += 1
+
+        self.formatter = formatter
+        self.output = output_object
+        self.skip = skip
+        if header:
+            self.skip -= 1
+        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
+