[Biocorba-l] SeqFeatureLocation

[Jason Stajich]

Alan - I've finally gotten a chance to think about the location model some
more.. 

I like the SeqFeatureLocation has 2 SeqFeaturePositions for start end, and
SeqFeaturePosition can handle all the codes.  But I want to be sure that
the following cases can really be handled by this.  Correct me if any of
these are wrong.  I think we might need another field to represent whether
or not the fuzzy code that is BEFORE or AFTER is also on the 3' or 5'
strand... Or we change the code to be BEFORE-3' BEFORE-5', AFTER-3',
AFTER-5'.  Yuck, I know... 

1..100 --  Location has 2 position objects for start and end fuzzy code is
           'EXACT', extension = 0
(1.2)..30 -- start is a position with fuzzy code 'WITHIN', position = 1,
             extension = 2 
1^3       -- is this a legal location?  If it is , how do we represent it?
<20..40   -- (feature starts before bp 20 on 5' strand), position=20
              extension=0, fuzzy='BEFORE'
>20..100  -- (feature starts after bp 20 on 5' strand) fuzzy='AFTER'
20<..100  -- (feature starts before bp 20 on 3' strand) fuzzy='BEFORE'
20>..100  -- (feature starts after bp 20 on 3' strand)  fuzzy='AFTER'

see 
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#FeaturesB
for explaination

"The location of each feature is provided as well, an can be a single
base, a contiguous span of bases, a joining of sequence spans, and
other representations.  If a feature is located on the complementary
strand, the word "complement" will appear before the base span. If the
"<" symbol precedes a base span, the sequence is partial on the 5' end
(e.g., CDS <1..206).  If the ">" symbol follows a base span, the
sequence is partial on the 3' end (e.g., CDS 435..915>)."


Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/