[DAS] Bio::Das segment information

[Lincoln Stein]

Sounds like a bug in the module.  I will fix.

Lincoln

On Friday 11 October 2002 06:03 am, Tony Cox wrote:
> Dear all,
>
> I'm having a little trouble getting some segment info out of a DAS server
> using the Bio::Das module - perhaps somebody can tell me if I am barking up
> the wrong tree.
>
> I want to compare the versions of a clone between two DAS-enabled
> databases. For a particular region I make a list of clones and request
> these from the second server. I'm not interested in features on the
> segments, merely the segment version field. Therefore I request the
> segments with a type qualifier that ensures I get back and empty segment
> (since I don't want to parse thousands of features just to get the segment
> ID/version from just one of them)
>
> It appears that the BIO::Das 'features' call only triggers the creation of
> a segment object when that segment has features. If I get back a DAS
> response of:
>
> <?xml version='1.0' standalone='no' ?>
> <!DOCTYPE DASGFF SYSTEM 'dasgff.dtd' >
> <DASGFF>
>   <GFF version="1.0"
> href="http://ecs3.internal.sanger.ac.uk:8080/das/vega10/features?segment=AL
>049767;segment=AL035660;type=static_golden_path"> <SEGMENT id="AL035660"
> version="16" start="1" stop="63795" />
>     <SEGMENT id="AL049767" version="12" start="1" stop="99746" />
>   </GFF>
> </DASGFF>
>
> no feature objects are built by the parser. This effectively blocks access
> to the segment data whick I am interested in or have I got this wrong? I
> could remove the type specifier but then I would have to parse (and throw
> away) all the features just to get the version.
>
> If so, what do you recommend as the best (and "cheapest") way to retrieve a
> segments version number?
>
> thanks
>
> Tony
>
>
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> Tony Cox			Email:avc@sanger.ac.uk
> Sanger Institute		WWW:www.sanger.ac.uk
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