Adds class for uncompressing transparently compressed files on line

python/obitools3/files/uncompress.pxd

@@ -0,0 +1,16 @@
+#cython: language_level=3
+
+cdef class MagicKeyFile:
+    cdef str    stream_mode
+    cdef object binary
+    cdef bytes  key 
+    cdef int    keylength
+    cdef int    pos
+    
+    cpdef bytes read(self,int size=?)
+    cpdef int tell(self)
+
+    
+cdef class CompressedFile:
+    cdef object accessor
+    

python/obitools3/files/uncompress.pyx

@@ -0,0 +1,111 @@
+#cython: language_level=3
+
+'''
+Created on 28 mars 2016
+
+@author: coissac
+'''
+
+import zipfile
+import bz2
+import gzip
+
+import io
+
+cdef class MagicKeyFile:
+    def __init__(self,stream,length=2):
+        
+        self.stream_mode = None
+        if hasattr(stream, "mode"):
+            self.stream_mode = stream.mode
+            if 'b' in stream.mode:
+                binary=stream
+            elif hasattr(stream, "buffer") and 'b' in stream.buffer.mode:
+                binary=stream.buffer
+            else:
+                self.stream_mode = None
+                
+        if self.stream_mode is None:
+            raise TypeError("stream does not present the good interface")
+        
+        self.binary=binary
+        self.key=binary.read(length)
+        self.keylength=length
+        self.pos=0
+        
+    cpdef bytes read(self,int size=-1):
+        cdef bytes r
+        
+        if self.pos < self.keylength:
+            if size > (self.keylength - self.pos):
+                size = size - self.keylength + self.pos
+                r = self.key[self.pos:] + self.binary.read(size)
+                self.pos=self.keylength + 1
+            elif size >=0 :
+                r = self.key[self.pos:(self.pos+size)]
+                self.pos+=size
+            else:
+                r = self.key[self.pos:] + self.binary.read(size)
+                self.pos=self.keylength + 1
+        else:
+            r = self.binary.read(size)
+            
+        return r
+    
+    cpdef int tell(self):
+        cdef int p
+        
+        if self.pos < self.keylength:
+            p = self.pos 
+        else:
+            p = self.tell()
+        
+        return p
+    
+    def __getattr__(self,name):
+        return getattr(self.binary, name)
+        
+
+    
+cdef class CompressedFile:
+    
+    
+    def __init__(self,stream):
+        cdef int            keylength
+        cdef MagicKeyFile   magic
+        cdef str            compressor
+        cdef bytes          k 
+        cdef object         c
+        
+        cdef dict compress = { 'zip' : (b'\x50\x4b\x03\x04',zipfile.ZipFile),
+                               'bz2' : (b'\x42\x5a\x68',bz2.BZ2File),
+                               'gz'  : (b'\x1f\x8b\x08',gzip.open)
+                   }
+        
+        keylength = max([len(x[0]) for x in compress.values()])
+        magic=MagicKeyFile(stream,keylength)
+        
+        self.accessor = None
+        
+        for compressor in compress:
+            k,c = compress[compressor]
+            if magic.key.startswith(k):
+                self.accessor = c(magic)
+        
+        if self.accessor is None:
+            self.accessor = magic
+            
+            
+        if 'b' not in magic.stream_mode:
+            self.accessor = io.TextIOWrapper(self.accessor)
+        
+    
+    def __getattr__(self,name):
+        return getattr(self.accessor, name)
+    
+    def __iter__(self):
+        for x in self.accessor:
+            yield x
+    
+
+