From 646f3d5f72ffb1782c396490c3e7f4bb37747e7a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 19 Feb 2008 16:53:40 +0000
Subject: [PATCH] code refactoring to rename oligo to word

---
 src/obitools/word/__init__.py | 33 +++++++++++++++++++++++++++++++--
 src/obitools/word/options.py  |  4 ++--
 src/obitools/word/predicat.py |  2 +-
 3 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/src/obitools/word/__init__.py b/src/obitools/word/__init__.py
index e9b2723..ed8b83a 100644
--- a/src/obitools/word/__init__.py
+++ b/src/obitools/word/__init__.py
@@ -3,7 +3,36 @@ from itertools import imap
 
 _dna='acgt'
 
-def wordIterator(size,_prefix=''):
+def wordCount(liste):
+    count = {}
+    
+    for e in liste:
+        count[e]=count.get(e,0) + 1
+    
+    return count
+
+
+def wordIterator(sequence,lword,step=1,endIncluded=False,circular=False):
+    assert not (endIncluded and circular), \
+      "endIncluded and circular cannot not be set to True at the same time"
+      
+    L = len(sequence)
+    sequence = str(sequence)
+    if circular:
+        sequence += sequence[0:lword]
+        pmax=L
+    elif endIncluded:
+       pmax=L
+    else:
+       pmax = L - lword + 1
+    
+    pos = xrange(0,pmax,step)
+    
+    for x in pos:
+        yield sequence[x:x+lword]
+
+
+def allWordIterator(size,_prefix=''):
     '''
     Iterate thought the list of all DNA word of
     size `size`.
@@ -18,7 +47,7 @@ def wordIterator(size,_prefix=''):
     '''
     if size:
         for l in _dna:
-            for w in wordIterator(size-1,_prefix+l):
+            for w in allWordIterator(size-1,_prefix+l):
                 yield w
     else:
         yield _prefix
diff --git a/src/obitools/word/options.py b/src/obitools/word/options.py
index cbb790f..1133cbc 100644
--- a/src/obitools/word/options.py
+++ b/src/obitools/word/options.py
@@ -2,8 +2,8 @@ from logging import debug,root,DEBUG
 
 
 
-from obitools.oligo import wordSelector,wordIterator
-from obitools.oligo import predicat
+from obitools.word import wordSelector,wordIterator
+from obitools.word import predicat
 
 
 
diff --git a/src/obitools/word/predicat.py b/src/obitools/word/predicat.py
index beb6620..a744f2c 100644
--- a/src/obitools/word/predicat.py
+++ b/src/obitools/word/predicat.py
@@ -1,5 +1,5 @@
 import re
-from obitools.oligo import wordDist
+from obitools.word import wordDist
 
 def rePredicatGenerator(regex):
     regex = re.compile(regex,re.I)