[DAS] Bio::Das segment information

[Tony Cox]

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=AL049767;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
Wellcome Trust Genome Campus	Webmaster
Hinxton				Tel: +44 1223 834244
Cambs. CB10 1SA			Fax: +44 1223 494919
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