[BioRuby] Beautiful code for Bioinformatics

Raoul Bonnal bonnal at ingm.org
Mon Feb 13 05:46:26 EST 2012 

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

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