[DAS] Coordinate systems

[Oliver Lyttelton]

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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