[BioRuby] A new plugin: bio-genomic-interval

[Pjotr Prins]

Good thinking. And I am glad to see biogem encourage modular design;
that is what we set out to achieve.

Pj.

On Sat, Apr 23, 2011 at 11:12:11PM +0900, MISHIMA, Hiroyuki wrote:
> Hi Jan and BioRuby-ML,
>
> Thank you your comment on the bio-genomic-interval library.
>
> After I have released bio-genomic-interval, I found Jan's ruby-ucsc-api  
> and the Slice class. The Slice class also plays an important role in the  
> Ruby Ensembl API.
>
> In conclusion, I think that it is good to merge my bio-genomic-interval
> into the Slice class and make a BioRuby plugin like "bio-slice" to share
> among libraries. To do this, we have to separate ensemble/core/slice.rb
> into common methods to share and the Ensembl API specific methods.
>
> The strong points of the Slice class are including the followings:
> * Using BioRuby objects such as Bio::Sequence::NA.
> * Slice#excise, #sub_slice, and #split
> * A short simple class name (Matz says "Name is important")
>
> So far, I use bio-genomic-interval in bio-ucsc-api because
> bio-genomic-interval has methods to convert between the common "1-based
> full-closed" and UCSC-internal "0-based half-closed" intervals. This
> conversion is trivial arithmetic but prevents bugs.
>
> Other methods only in GenomicInterval are the followings:
> #parse (parses UCSC style "chr1:1,234-3,456")
> #comparison (returns :left_adjacent [i.e. distance <20bp], :left_off,
> :contains, :left_overlapped etc.)
> #overlap (returns a distance or an overlap-length between two intervals)
> #expand (returns a minimum interval containing two intervals),
> #center (returns a center position)
>
> Sincerely yours,
> Hiro.
>
> Jan Aerts wrote (2011/04/23 18:31):
>> Hi Hiro,
>>
>> You might take a look at the Slice class in the ruby-ensembl-api at
>> https://github.com/jandot/ruby-ensembl-api/blob/master/lib/ensembl/core/slice.rb.
>> This has very similar functionality, and might give some additional
>> ideas as well, for example:
>>
>> - Slice#overlaps?(other_slice) => checks whether 2 slices overlap
>> - Slice#within?(other_slice) => checks whether this slices is contained
>> within another slice
>> - Slice#contains?(other_slice) => checks whether this slices contains
>> another slice
>> - Slice#excise(array_of_regions) => takes a slices and removes a certain
>> region, returning an array of smaller slices. For example:
>>
>> # original_slice = Slice.new('chrX',1,10000)
>> # new_slices = original_slice.excise([500..750, 1050..1075])
>> # new_slices.each do |s|
>> #   puts s.display_name
>> # end
>> #
>> # # result:
>> # # chromosome:X:1:499:1
>> # # chromosome:X:751:1049:1
>> # # chromosome:X:1076:10000:1
>>
>> - Slice#sub_slice(start, stop) => creates a truncated version of this slice
>> - Slice#split(length, overlap) => splits a slice into smaller bits (e.g.
>> creates an array of slices of 100bp long), optionally with an overlap
>> between the resultant slices.
>>
>> Just my 2c. (Also: if you have feature requests, ideas or other comments
>> for the ruby-ensembl-api, see rubyensemblapi.userecho.com
>> <http://rubyensemblapi.userecho.com>)
>>
>> jan.
>
> -- 
> MISHIMA, Hiroyuki, DDS, Ph.D.
> COE Research Fellow
> Department of Human Genetics
> Nagasaki University Graduate School of Biomedical Sciences
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