[BioRuby] Beautiful code for Bioinformatics

Raoul Bonnal bonnal at ingm.org
Mon Feb 13 10:37:20 UTC 2012


Thanks Francesco,
You have cute code in BioNGS as well. I like the piece of code which saves
in an history file the commands executed by the user:

https://github.com/helios/bioruby-ngs/blob/master/lib/bio/ngs/task.rb

Every time the user runs biongs the command line is cached, the original
idea was to save the commands to create a workflow on the fly. It is another
example of Monkey Patching with injection of new code.

On 13/02/12 11.06, "Francesco Strozzi" <francesco.strozzi at gmail.com> 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/f33abf9bbd90c3c1e320f06447fdb54ffd0
>> 94c5d
>>>> 
>>>> 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
>> 
> 
> 





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