+ parser works now with mmap and sscanf

[qpalma.git] / python / computeSpliceAlign.py

diff --git a/python/computeSpliceAlign.py b/python/computeSpliceAlign.py
index 04cbbe1..a6d4a49 100644 (file)
--- a/python/computeSpliceAlign.py
+++ b/python/computeSpliceAlign.py
@@ -4,7 +4,6 @@
 from numpy.matlib import zeros
 import pdb
 
-
 def  computeSpliceAlign(dna, exons):
    """
    Exonpos: Anfang Exon bis 1 rechts neben Ende Exon
@@ -19,6 +18,7 @@ def  computeSpliceAlign(dna, exons):
    numberOfExons = (exons.shape)[0] # how many rows ?
    exonSizes = [-1]*numberOfExons
 
+   assert numberOfExons == 3
 
    for idx in range(numberOfExons):
       exonSizes[idx] = exons[idx,1] - exons[idx,0]
@@ -29,30 +29,19 @@ def  computeSpliceAlign(dna, exons):
    # 1:donorpos, 3:intron 2:acceptorpos, 0:exon, 4: dangling end
    SpliceAlign = []
 
-   if exons[0,0] > 1:
+   if exons[0,0] > 0:
       SpliceAlign.extend([4]*(exons[0,0]))
 
-   #for i=1:nr_exons
-   #  exon_length = exon_sizes(i); %exons(i,2) is begin of intron
-   #  SpliceAlign = [SpliceAlign, zeros(1,exon_length)] ;
-   #  if i~= nr_exons,
-   #    intron_length = exons(i+1,1) - exons(i,2) ;
-   #    SpliceAlign = [SpliceAlign, 1, ones(1,intron_length-2)*3, 2] ;
-   #  end
-   #end 
-
    for idx in range(numberOfExons):
       exonLength = exonSizes[idx]
       SpliceAlign.extend([0]*exonLength)
       
       if idx < numberOfExons-1:
          intronLength = exons[idx+1,0] - exons[idx,1]
-         SpliceAlign.extend([1])
-         SpliceAlign.extend([3]*((intronLength-2)))
-         SpliceAlign.extend([2])
-         
+         SpliceAlign.extend([1]+[3]*(intronLength-2)+[2])
+
    if len(dna) > exons[2,1]:
-      SpliceAlign.extend([4]*(len(dna)+1-exons[2,1]))
+      SpliceAlign.extend([4]*(len(dna)-exons[2,1]))
 
    assert len(SpliceAlign) == len(dna), pdb.set_trace()