[BioRuby] Beautiful code for Bioinformatics
Mic
mictadlo at gmail.com
Mon Feb 13 23:33:04 EST 2012
Hi,
Did anyone try out
* GO: http://en.wikipedia.org/wiki/Go_(programming_language)
* Rust: http://en.wikipedia.org/wiki/Rust_(programming_language)
* Vala: http://en.wikipedia.org/wiki/Vala_(programming_language)
On Mon, Feb 13, 2012 at 8:46 PM, Raoul Bonnal <bonnal at ingm.org> wrote:
> Yeah, I was thinking the exact same thing.
>
> This kind of documentation will be of great help!!! I'm thinking about
> teaching Ruby @ Uni.
>
> What I missed from the previous email is:
> Beautiful code come from coders but that is not enough, working with people
> in this ML I found that the quality of code and its beauty increase only if
> you chat/talk with people and you are available to accept critics and
> contributes.
>
> Another tab ? ;-)
>
>
> On 13/02/12 11.34, "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/uti
> >>> l/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/f33abf9bbd90c3c1e320f06447fdb54ffd
> >>> 094c5d
> >>>>>
> >>>>> 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
>
>
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>
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