Trying to eliminate a loop

*To*: mathgroup at smc.vnet.net*Subject*: [mg50595] Trying to eliminate a loop*From*: János <janos.lobb at yale.edu>*Date*: Sat, 11 Sep 2004 06:45:09 -0400 (EDT)*Sender*: owner-wri-mathgroup at wolfram.com

Hi, I have a four letter alphabet: In[3]:= baseAlphabet={a,t,c,g} I can create an arbitrary length list from it with: generateRandomStrand[alphabet_List, len_Integer] := \ Table[alphabet[[Random[Integer, {1, Length[alphabet]}] ]], {len}]; for example: ls = generateRandomStrand[baseAlphabet, 23460]; I want to know what kind of primerLength=7 sub-strands are in it, so I partition it: lspr = Partition[ls, primerLength, 1]; All the possible sub-strands form a set: primerSet=Distribute[Table[baseAlphabet, {primerLength}], List]; << Statistics`DataManipulation` freq=Frequencies[lspr]; gives me a frequency distribution, that is what elements of primerSet occur at what frequency in lspr: To know which sublist occurs the most I do: In[64]:= pr=Flatten[First[Extract[freq[[All, 2]], Split[Position[freq, Max[freq[[All, 1]]]][[All, 1]] ]] ]] Out[64]= {a,a,c,t,g,c,g} and it is at positions In[65]:= prpos=Position[lspr,pr] Out[65]= {{2860},{4336},{6791},{11387},{12164},{17472},{17833},{17954}} in lspr and in ls. At those positions in ls I want to attach the complement of this pr sublist, so I create the following rules: complementRule = {a -> t, c -> g, t -> a, g -> c}; replaceWithComplement = {a -> {a, t}, c -> {c, g}, t -> {t, a}, g -> {g, c}} I created a For loop which at prpos replaces the elements there with the double elements indicated by the rule above on primerLength intervals of ls: For[i = 1, i ² Length[pr], i++, ls = ReplacePart[ls, replaceWithComplement, prpos + i - 1, \ Flatten[Position[replaceWithComplement, {Part[Extract[ls, prpos + i - 1], 1], Part[Extract[ ls, prpos + i - 1], 1] /. complementRule}]]] ] Mathematica does this For loop in about 0.046678 Second on my machine. With primerLength=9 it is 0.050748 Second - pr had just three positions on the strand. I have the feeling that it can be done faster with Map or MapAt, so the For loop could go away. I also do not like that I have to rewrite ls in every cycle. ReplacePart does not look good to me in this situation, but I have not find yet the way to apply the replaceWithComplement rule directly to the primerLength long intervals of ls at prpos positions. Any good tip ? Thanks ahead, J?nos ---------------------------------------------- Trying to argue with a politician is like lifting up the head of a corpse. (S. Lem: His Master Voice)

**Follow-Ups**:**Re: Trying to eliminate a loop***From:*DrBob <drbob@bigfoot.com>

**Re: Trying to eliminate a loop***From:*DrBob <drbob@bigfoot.com>