[BioRuby] locus mixin

[Naohisa GOTO]

Hi,

On Fri, 12 Jun 2009 10:53:08 +0100
Jan Aerts <jan.aerts at gmail.com> wrote:

> What do people think about adding a IsLocus mixin to bioruby? For a lot of
> my work I need to check if genes or polymorphisms or clones or ... overlap.
> I use the IsLocus mixin to get that done. Any object that has a chromosome,
> start and stop can have the module mixed in. Some of the methods as I have
> them defined locally:

What classes are considered the module to be mixed in?
In BioRuby, as far as I know, there are currently no classes
which have all of these methods simultaneously.

I think only putting a mixin is not a good way. It is better to
prepare some classes which can handle real data (which can probably
be downloaded from famous genome/expression data repositories) and
can perform typical tasks conveniently.

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

> module IsLocus
>   def range
>     return Range.new(self.start, self.stop)
>   end
> 
>   def overlaps?(other_locus)
>     return false if self.chromosome != other_locus.chromosome
> 
>     if self.range.overlaps?(other_locus.range)
>       return true
>     end
> 
>     return false
>   end
> 
>   def contained_by?(other_locus)
>     return false if self.chromosome != other_locus.chromosome
> 
>     if self.range.contained_by?(other_locus.range)
>       return true
>     end
> 
>     return false
>   end
> 
>   def contains?(other_locus)
>     return false if self.chromosome != other_locus.chromosome
> 
>     if self.range.contains?(other_locus.range)
>       return true
>     end
> 
>     return false
>   end
> 
>   def to_s
>     return self.chromosome + ':' + self.range.to_s
>   end
> 
>   def to_gff3
>     return [self.chromosome, self.class.name, self.start, self.stop, '.',
> '.', '.', 'ID=' + self.id.to_s].join("\t")
>   end
> 
>   def to_bed
>     if self.respond_to?(:name)
>       return [self.chromosome, self.start, self.stop, self.name].join("\t")
>     else
>       return [self.chromosome, self.start, self.stop, self.class.name + '_'
> + self.id.to_s].join("\t")
>     end
>   end
> 
>   # The following makes it possible to call Gene#to_bed which would dump all
> Gene objects in BED format
>   def self.included mod
>     class << mod
>       def to_bed
>         output = Array.new
>         output.push("track name='#{self.name}' description='#{self.name}'")
>         self.all.each do |record|
>           output.push record.to_bed
>         end
>         return output.join("\n")
>       end
>     end
>   end
> end
> 
> Let me know what you think,
> jan.
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