[DAS] Coordinate systems

[Lincoln Stein]

There is a lot of coordinate conversion involved.  Are you using any
particular toolkit, such as Dazzle?  This should make coordinate
conversion easier.

The Perl equivalent for coordinate conversion is not done, but is high
up on the to-do list.

Lincoln

Oliver Lyttelton writes:
 > 
 > 
 > Dear all,
 >     I am trying programatically to retrieve all the local feature 
 > information 50,000bp upstream and downstream) of a location specified 
 > relative to an NT segment.
 > 
 > This is what I think I need to do:-
 > 
 > Use
 > 
 > http://servlet.sanger.ac.uk:8080/das/ensembl729/features?segment=NT_030792
 > 
 > to retrieve features direct from the NT segment.
 > 
 > This will give me a list of all features including a load of static_golden 
 > path records.
 > 
 > I then need to requery  the ref sequence ensembl729 using segment=XXX for 
 > each XXX which is one of the static_golden_path identifiers.
 > 
 > For these segments I need to convert them back up into the NT coordinate 
 > system. I'm not quite sure how to do this as sometimes it seems you need to 
 > subtract the contig coordinate system from the end of the nt coordinate 
 > system rather than adding it to the start. I thought this was dependent on 
 > the orientation, but it seems more complicated than this. Is there a 
 > document somewhere that explains how to do the conversions as I am lost.
 > 
 > To get the NCBI stuff I need to get the name of the chromosome the NT is 
 > from from somewhere? Then I can query each of the ncbi data sources with the 
 > chromosome number as the segment Id. I will then have to reconvert the 
 > relevant features into the NT coordinate system.
 > 
 > As you may have gathered, what seemed like a straightforward task is getting 
 > a bit colosal and any tips pointing me towards an easier solution would be 
 > greatly appreciated. The main problem seems to be that features are only 
 > specified relative to one of the coordinate systems and all three are used 
 > so a conversion is necessary.???
 > 
 > Many thanks for your help with this,
 > 
 > Oliver
 > 
 > 
 > 
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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