Talk:BioPerl Locations

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NOTE: Much of this is to sort out (at least in my mind) how Locations are used within BioPerl and how they might be reimplemented in the future (think of it as half HOWTO, half opinion piece). The below are my scattered thoughts on the subject, in no particular order. --Chris Fields 16:20, 3 November 2009 (UTC)

  • thanks for adding this cjf, very enlightening-- (I was looking for ugg boots, when I happened on it) --maj 17:22, 4 November 2009 (UTC)

PS: This is also to help drive the Moose-based implementation of Locations.

Contents

Bio::LocationI

In a general sense, Locations are glorified Ranges that define a specific sequence, in that they have a defined start/end/strand. However, the start and end coordinates may not be simple integers (they can be open-ended, or 'fuzzy'), the coordinates may be inclusive, exclusive, or somewhere between (as defined by the Bio::Location::CoordinatePolicyI).

Methods specific to this interface:

Bio::Location::Atomic

Bio::Location::Simple

Bio::Location::SplitLocationI

This is a Bio::LocationI that is also a collection of subLocations.

Methods specific to this interface:

Bio::Location::Split

I think it would be helpful if we mentioned somewhere in this section that the safest way to access sub-locations is with Bio::Location::Split::each_Location . It took me a while to figure out how to get sublocations out of a genbank seqIO object with sub_Location, then I had a problem where I ran into a gene with only one exon and sub_Location died (not very gracefully). Newbies like myself look to this website for documentation. Flies 19:36, 10 February 2011 (UTC)

As I mentioned on the original page and at the top of this one, this isn't made for primary user consumption. The point of the original page (originally developed several years ago) was to create a page which may at some point be integrated into current documentation or would live on it's own. That hasn't happened yet, but we gladly accept any help along those lines. --Chris Fields 16:34, 11 February 2011 (UTC)

Bio::Location::FuzzyLocationI

Methods specific to this interface:

Bio::Location::Fuzzy

Bio::Location::CoordinatePolicyI

Bio::Factory::FTLocationFactory

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