From: Maurizio Cirilli <mauricirl@...>
Date: 2010-10-28T17:45:35+09:00
Subject: Re: Extraction of single subarrays from multidimensional array

Dear Jesus,  YES this this exactly what I wanted to do. Reading your
dense end elegant code, I understood how I was trying to use a wrong
approach in writing my own program although some parts of your
syntax is still obscure to me. I will study them.
I wish to thank all the people who replied to my question offering
their
so valuable help.

-- Maurizio


On Oct 27, 6:07 pm, Jesús Gabriel y Galán <jgabrielyga...@gmail.com>
wrote:
> On Wed, Oct 27, 2010 at 2:05 PM, Maurizio Cirilli <mauric...@gmail.com> wrote:
> > Dear Robert,
>
> >   this is I want to do:
>
> > (1) extract subarrays from a md-arrays (but the number of subarrays
> >     can vary from case to case)
> > (2) use separated subarrays to make all possible nucleotide sequences
> >     is possible to build from them permutating the codons at each
> > position
> >     (row) i.e. all the 6*2*6 sequences 9 nucleotide long in my
> > example
> > (3) convert them to string and put in a single array ( this is
> > required for
> >     compatibility with BioRuby classes and methods that deal withDNA
> >     sequences as strings)
> > (4) make further analysis on these sequences by BioRuby.
>
> Looking around for permutations in Ruby, I came acrosshttp://snippets.dzone.com/posts/show/3332
> and adapting it a little bit for your use case, I came up with:
>
> class Array
>   def sequence(i = 0, *a)
>     return a.join if i == size
>     self[i].map {|x| sequence(i+1, *(a + [x]))}
>   end
> end
>
> ss = [["tcg", "agt", "tct", "agc", "tca", "tcc"],
>          ["aaa", "aag"],
>          ["ctg", "tta", "ctt", "cta", "ctc", "ttg"]]
>
> p ss.sequence.flatten
>
> $ ruby permutations.rb
> ["tcgaaactg", "tcgaaatta", "tcgaaactt", "tcgaaacta", "tcgaaactc",
> "tcgaaattg", "tcgaagctg", "tcgaagtta", "tcgaagctt", "tcgaagcta",
> "tcgaagctc", "tcgaagttg", "agtaaactg", "agtaaatta", "agtaaactt",
> "agtaaacta", "agtaaactc", "agtaaattg", "agtaagctg", "agtaagtta",
> "agtaagctt", "agtaagcta", "agtaagctc", "agtaagttg", "tctaaactg",
> "tctaaatta", "tctaaactt", "tctaaacta", "tctaaactc", "tctaaattg",
> "tctaagctg", "tctaagtta", "tctaagctt", "tctaagcta", "tctaagctc",
> "tctaagttg", "agcaaactg", "agcaaatta", "agcaaactt", "agcaaacta",
> "agcaaactc", "agcaaattg", "agcaagctg", "agcaagtta", "agcaagctt",
> "agcaagcta", "agcaagctc", "agcaagttg", "tcaaaactg", "tcaaaatta",
> "tcaaaactt", "tcaaaacta", "tcaaaactc", "tcaaaattg", "tcaaagctg",
> "tcaaagtta", "tcaaagctt", "tcaaagcta", "tcaaagctc", "tcaaagttg",
> "tccaaactg", "tccaaatta", "tccaaactt", "tccaaacta", "tccaaactc",
> "tccaaattg", "tccaagctg", "tccaagtta", "tccaagctt", "tccaagcta",
> "tccaagctc", "tccaagttg"]
>
> Which if I understood correctly solves your steps 1 to 3.
>
> Hope this helps,
>
> Jesus.