perdiction in python

gistfile1.py

import sys,string
from numpy import *
from matplotlib import *

#read sequences
#sequences are stored in many lines
f=open(sys.argv[1], 'r')
seq=[]
for line in f.readlines():
    seq.append(string.strip(line));

def delta(l,m):
    delta=0;
    if l=='A' and m=='U':
        return 1;
    elif l=='U' and m=='A':
        return 1;
    elif l=='G' and m=='C':
        return 1;
    elif l=='C' and m=='G':
        return 1;
    else:
        return 0;

def buildDP(seq):
    L=len(seq);
    s=zeros((L,L));
    for n in xrange(1,L):
        for j in xrange(n,L):
            i=j-n;
            case1=s[i+1,j-1]+delta(seq[i],seq[j]);
            case2=s[i+1,j];
            case3=s[i,j-1];
            if i+3<=j:
                tmp=[];
                for k in xrange(i+1,j):
                    tmp.append(s[i,k]+s[k+1,j]);
                case4=max(tmp);
                s[i,j]=max(case1,case2,case3,case4);
            else:
                s[i,j]=max(case1,case2,case3);
    return s;

def traceback(s,seq,i,j,pair):
    if i<j:
        if s[i,j]==s[i+1,j]:
            traceback(s,seq,i+1,j,pair);
        elif s[i,j]==s[i,j-1]:
            traceback(s,seq,i,j-1,pair);
        elif s[i,j]==s[i+1,j-1]+delta(seq[i],seq[j]):
            pair.append([i,j,str(seq[i]),str(seq[j])]);
            traceback(s,seq,i+1,j-1,pair);
        else:
            for k in xrange(i+1,j):
                if s[i,j]==s[i,k]+s[k+1,j]:
                    traceback(s,seq,i,k,pair);
                    traceback(s,seq,k+1,j,pair);
                    break;
    return pair;

for q in xrange(0,len(seq)):
    pair=traceback(buildDP(seq[q]),seq[q],0,len(seq[q])-1,[])
    print "max # of folding pairs: ",len(pair);
    for x in xrange(0,len(pair)):
        print '%d %d %s==%s' % (pair[x][0],pair[x][1],pair[x][2],pair[x][3]);
    print "---";