ADD: new option --fieldcutname to make ecoTag work with paired-end sequences (experimental)

src/ecoTag.py

@@ -102,6 +102,12 @@ def addSearchOptions(optionManager):
                              default=0.0,
                              help='Tolarated rate of wrong assignation')    
 
+    optionManager.add_option('-F','--fieldcutname',
+                             action='store',dest='fieldcutname',
+                             default=None,
+                             help="""Turn Unassembled match mode 'ON' when 'fieldcutname' is a tag of the sequence. 
+                                     This tag gives the position of the junction of the two reads in the sequence (on (Celine + Fred) parle trop bien anglais !)""")    
+
 
 def count(data):
     rep = {}
@@ -121,6 +127,34 @@ def count(data):
         rep[k]=rep.get(k,default)+v
     return rep
 
+
+from obitools.location import SimpleLocation
+def myLenlcs(s1, s2, fieldCutName, minid, normalized, reference):
+
+    if (fieldCutName is not None) and (s1.hasKey(fieldCutName)) :
+
+        cutPos   = s1[fieldCutName]
+        locs1_5P = SimpleLocation(1,cutPos)
+        locs1_3P = SimpleLocation(cutPos+1,len(s1))
+        
+        locs2_5P = SimpleLocation(1, min(cutPos, len(s2)))
+        locs2_3P = SimpleLocation(max(1, len(s2)-(len(s1)-cutPos)+1), len(s2))
+        
+        overlap = min(0,len(s1) - len(s2))
+             
+        lcs5P, lali5P = lenlcs(s1.getSubSeq(locs1_5P),s2.getSubSeq(locs2_5P),minid,False)
+        lcs3P, lali3P = lenlcs(s1.getSubSeq(locs1_3P),s2.getSubSeq(locs2_3P),minid,False)
+
+        raw_lcs  = lcs5P  + lcs3P  - overlap
+        lali = lali5P + lali3P - overlap
+        lcs = raw_lcs / float(lali)
+        
+    else:     
+        lcs, lali = lenlcs(s1,s2,minid,normalized,reference)
+
+    return lcs, lali
+
+
 def lcsIterator(entries,db,options):
     
     for seq in entries:
@@ -128,7 +162,7 @@ def lcsIterator(entries,db,options):
         maxid   = (None,0.0)
         minid   = options.minimum
         for d in db:
-            lcs,lali = lenlcs(seq,d,minid,normalized=True,reference=ALILEN)
+            lcs,lali = myLenlcs(seq, d, options.fieldcutname, minid,normalized=True,reference=ALILEN)
             if lcs > maxid[1]:
                 maxid = (d,lcs)
                 minid = maxid[1] ** options.shape
@@ -145,7 +179,7 @@ def lcsIteratorSelf(entries,db,options):
         maxid   = ([],0.0)
         minid   = options.minimum
         for d in db:
-            lcs,lali = lenlcs(seq,d,minid,normalized=True,reference=ALILEN)
+            lcs,lali = myLenlcs(seq,d,options.fieldcutname,minid,normalized=True,reference=ALILEN)
             if lcs > maxid[1]:
                 maxid = ([d],lcs)
                 minid = maxid[1]