ps3c.py

def constrainedMatchPair(firstMatch, secondMatch, length):
    constrainedList = []
    for i in range(len(firstMatch)):
        for j in range(len(secondMatch)):
            if secondMatch[j] == firstMatch[i] + length + 1:
                constrainedList.append(firstMatch[i])
    constrainedTuple = tuple(constrainedList)
    return constrainedTuple

def subStringMatchOneSub(key,target):
    """search for all locations of key in target, with one substitution"""
    allAnswers = ()
    for miss in range(0,len(key)):
        # miss picks location for missing element
        # key1 and key2 are substrings to match
        key1 = key[:miss]
        key2 = key[miss+1:]
        #print 'breaking key',key,'into',key1,key2
        # match1 and match2 are tuples of locations of start of matches
        # for each substring in target
        match1 = subStringMatchExact(target,key1)
        match2 = subStringMatchExact(target,key2)
        # when we get here, we have two tuples of start points
        # need to filter pairs to decide which are correct
        filtered = constrainedMatchPair(match1,match2,len(key1))
        allAnswers = allAnswers + filtered
        #print 'match1',match1
        #print 'match2',match2
        #print 'possible matches for',key1,key2,'start at',filtered
    return allAnswers

##target1 = 'atgacatgcacaagtatgcat'
##target2 = 'atgaatgcatggatgtaaatgcag'

### key strings

##key10 = 'a'
##key11 = 'atg'
##key12 = 'atgc'
##key13 = 'atgca'

##print subStringMatchOneSub(key10,target1)
##print subStringMatchOneSub(key11,target1)
##print subStringMatchOneSub(key12,target1)
##print subStringMatchOneSub(key13,target1)
##print subStringMatchOneSub(key10,target2)
##print subStringMatchOneSub(key11,target2)
##print subStringMatchOneSub(key12,target2)
##print subStringMatchOneSub(key13,target2)