[BioRuby] new module map.rb

Moses M. Hohman mmhohman at northwestern.edu
Thu May 4 14:59:27 UTC 2006

Hi Jan,

Cool, I'll check it out. Do you have any unit tests for this?


On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote:

> Hi all,
> I've added a new module map.rb to the cvs repository that describes
> markers and maps (such as linkage maps, radiation hybrid maps and the
> sort):
> * Bio::Map::SimpleMap
> * Bio::Map::Marker
> * Bio::Map::Mapping
> * Bio::Map::ActsLikeMap
> * Bio::Map::ActsLikeMarker
> Two important design decisions were taken in writing these modules:
> (1) relationship map-mapping-marker:
> ------------------------------------
> In an early implementation, Map objects could have a list of Marker
> objects associated with them. However, a single Marker object can also
> be mapped to different Maps. As a result, to check which maps have a
> certain marker in common, all markers of all maps would have to be
> screened. Therefore, to facilitate this many-to-many relationship
> complication, I decided to put a Mapping object in between Map and
> Marker. Such a Mapping object has three things associated with it:  
> Map,
> Marker and location (which is a Bio::Location object).
> If a marker A is added to a map B, a Mapping object is created and  
> added
> to both the @mappings array in marker A, _and_ the @mappings array in
> map B.
> (2) mixins ActsLikeMap and ActsLikeMarker:
> ------------------------------------------
> Different things can be mapped to different things, or in other words:
> different things can act as markers or as maps.
> * can act as markers:
> ** a microsatellite: when it's mapped on a linkage group
> ** a clone: when it's mapped to the cytogenetic map (using FISH),  
> or if
> it's included in the physical map (FPC)
> ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone
> ** ...
> * can act as maps:
> ** a linkage group
> ** a radiation hybrid map
> ** a clone: when it has a BAC end sequence associated with it
> ** ...
> As it is nonsense to create a Marker class and have all these  
> different
> types of markers inherit from it (would a clone inherit from
> Bio::Marker, or from Bio::Map?), I created two modules that can be  
> mixed
> in with any class: Bio::Map::ActsLikeMap and Bio::Map::ActsLikeMarker.
> As a result, a Clone class (which doesn't exist yet) can include both,
> and have properties of a map _and_ a marker.
> Give it a go.
> PS: Thinking about what can act like a map or a marker: a sequence can
> essentially also be considered a map (we actually talk about it  
> that way
> in our department), with for example BLAST hits (or any other feature
> with a location) that act as markers. The unit of the map is 'bp'.
> Jan Aerts, PhD
> Bioinformatics Group
> Roslin Institute
> Roslin, Scotland, UK
> +44 131 527 4200
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