[BioRuby] Beautiful code for Bioinformatics

George Githinji georgkam at gmail.com
Mon Feb 13 05:36:25 EST 2012 

Good idea PJ!


On Mon, Feb 13, 2012 at 1:34 PM, Pjotr Prins <pjotr.public14 at thebird.nl> wrote:
> Excellent.
>
> May I propose that at least the other half of the authors of the
> Biogem paper send in an example of beautiful code? We can compile
> these snippets on a special page on one of the websites (or both).
> That will help courses, 'newbies' and even 'die hard' Perl users, such
> as Yoda, to see what this Ruby thing is about.
>
> Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh
> herh herh.
>
> Pj.
>
> On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote:
>> Some code I particularly liked comes from the BioNGS Wrapper library (by
>> Raoul). The gem is in development and I'm contributing to it so I could
>> look at the code from a very close perspective!
>>
>> https://gist.github.com/1815501
>>
>> What is interesting is the use of an internal DSL which makes the code
>> particularly expressive and readable, and writing a wrapper becomes only a
>> matter of defining the options that the command line binary expects. The
>> library is quite large and includes also methods to define aliases for the
>> options.
>> This module makes use also of the powerful Thor gem (used in Rails) to
>> create and define tasks that can be used to launch the binaries and to
>> include them in larger workflows and pipelines.
>> Now let's say you want to turn your freshly new wrapped binary into a
>> mighty Thor taks, all you need to do is:
>>
>> https://gist.github.com/1815523
>>
>> The amazing part is that the parameters passed to the block works like
>> arguments definition for the Thor task itself. The code that makes this
>> possible behind the scenes is here:
>>
>> https://gist.github.com/1815481
>>
>> It checks also if the number of arguments passed are equal to the arguments
>> of the block. If not, it raises an error to the user as he/she is calling
>> the task with the wrong number of arguments. To understand every part you
>> need to know a bit the way the Thor library defines tasks (more here:
>> https://github.com/wycats/thor) but the code here in BioNGS definitely
>> worth a look!
>>
>> P.S. I'm diving into Scala too :-). I took the Odersky book few months ago
>> and now I'm about to start looking in details at this new programming
>> language. Easy and powerful parallelism is the new goal we need to achieve
>> to keep up with the big data era.
>>
>> Cheers
>>
>> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins <pjotr.public14 at thebird.nl>wrote:
>>
>> > OK, here another candidate for the price of beautiful code:
>> >
>> >
>> > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
>> >
>> > Trevor has implemented some hairy logic into the RE code. I mean
>> > hairy, that if it were done by someone else it would become spaghetti
>> > code (plenty of examples there in the real world!). You can see, that
>> > even when choosing sensible names, and explaining the code with good
>> > comments, it may still be hard to understand! But I think
>> >
>> >  def add_cuts_from_cut_ranges(cut_ranges)
>> >
>> > pretty much sums it up :). Still, it is beautiful, because it is hard
>> > to think of doing it better. The Ruby code is short and self
>> > explanatory and RE library has almost become a DSL for cutting
>> > sequences using restriction enzymes. That is beautiful.
>> >
>> > Pj.
>> >
>> > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote:
>> > > Hi All
>> > > Beauty is in the eyes of the beholder!
>> > > The Bio-Alignment plugin can  read and interconvert a nucleotide
>> > > alignment to an amino acid alignment.  I liked the simplicity of how
>> > > PJ has implemented the codon to amino acid conversion helper method
>> > > while taking care of the gaps or undefined aa translations.
>> > >
>> > >       # lazily convert to Amino acid (once only)
>> > >       def to_aa
>> > >         aa = translate
>> > >         if not aa
>> > >           if gap?
>> > >             return '-'
>> > >           elsif undefined?
>> > >             return 'X'
>> > >           else
>> > >             raise 'What?'
>> > >           end
>> > >         end
>> > >         aa
>> > >       end
>> > >
>> > > This method does not have any ruby 'magic' and is self documenting.
>> > > The gap? and undefined? methods are implemented as simple one line
>> > > standalone methods.
>> > >
>> > > Again I like this simple 'trick' of getting an array of codons from a
>> > > sequence in the codonsequence class.
>> > >
>> > > seq.scan(/\S\S\S/) #gets an array of codons
>> > >
>> > > The longer alternative would be to create a bio::sequence::NA object
>> > > and iterate
>> > > seq = Bio::Sequence::NA.new("blahahahha")
>> > > seq.window_search(3, 3) do |subseq|
>> > >   puts subseq
>> > > end
>> > >
>> > > It seems more intuitive to represent a sequence as an array of codon
>> > > objects. In this way the codons have some state and can carry
>> > > 'luggage'. getting the string representation of the sequence is as
>> > > simple as
>> > > def to_s
>> > >  @seq.map { |codon| codon.to_s }.join(' ')
>> > > end
>> > >
>> > > To be more DRY, the to_nt method in the same class could be aliased
>> > > from the to_s method
>> > >
>> > > It seems the bio-plugins are a rich source of tricks and great
>> > learning.... !
>> > >
>> > >
>> > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock <p.j.a.cock at googlemail.com>
>> > wrote:
>> > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins <
>> > pjotr.public14 at thebird.nl> wrote:
>> > > >> Correct me if I am wrong, but has everyone moved across to BioPython
>> > > >> now? Or even to the dark side?
>> > > >>
>> > > >> Pj.
>> > > >
>> > > > I haven't noticed any BioRuby developers posting on the Biopython
>> > > > mailing lists recently - but you'd be welcome ;)
>> > > >
>> > > > On a related topic, my first BioRuby pull request was merged, so
>> > > > there is a little direct cross project contribution going on :)
>> > > >
>> > > >
>> > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d
>> > > >
>> > > > Peter
>> > > > _______________________________________________
>> > > > BioRuby Project - http://www.bioruby.org/
>> > > > BioRuby mailing list
>> > > > BioRuby at lists.open-bio.org
>> > > > http://lists.open-bio.org/mailman/listinfo/bioruby
>> > >
>> > >
>> > >
>> > > --
>> > > ---------------
>> > > Sincerely
>> > > George
>> > > Skype: george_g2
>> > > Blog: http://biorelated.wordpress.com/
>> > > Twitter: http://twitter.com/#!/george_l
>> > >
>> > _______________________________________________
>> > BioRuby Project - http://www.bioruby.org/
>> > BioRuby mailing list
>> > BioRuby at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioruby
>> >
>>
>>
>>
>> --
>>
>> Francesco
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby



-- 
---------------
Sincerely
George
Skype: george_g2
Blog: http://biorelated.wordpress.com/
Twitter: http://twitter.com/#!/george_l

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