A first version of the fasta parser

python/obitools3/parsers/fasta.pxd

@@ -0,0 +1,8 @@
+#cython: language_level=3
+
+from .header cimport parseHeader
+from ..files.universalopener cimport uopen
+from ..files.linebuffer cimport LineBuffer
+
+
+    

python/obitools3/parsers/fasta.pyx

@@ -0,0 +1,46 @@
+#cython: language_level=3
+
+'''
+Created on 30 mars 2016
+
+@author: coissac
+'''
+
+def fastaIterator(lineiterator, int buffersize=100000000):
+    cdef LineBuffer lb
+    cdef str        ident
+    cdef str        definition
+    cdef dict       tags
+    cdef list       s
+    
+    if isinstance(lineiterator,(str,bytes)):
+        lineiterator=uopen(lineiterator)
+    
+    if isinstance(lineiterator, LineBuffer):
+        lb=lineiterator
+    else:
+        lb=LineBuffer(lineiterator,buffersize)
+        
+    i = iter(lb)
+    line = next(i)
+    
+    while True:
+        ident,tags,definition = parseHeader(line)
+        s = []
+        line = next(i)
+        while line[0]!='>':
+            s.append(line[0:-1])
+            line = next(i)
+        sequence  = "".join(s)
+        quality   = None
+
+        yield { "id"         : ident,
+                "definition" : definition,
+                "sequence"   : sequence,
+                "quality"    : quality,
+                "tags"       : tags,
+                "annotation" : {}
+              }
+        
+        
+