Hi
I am trying to setup a custom mart db etc and have run into some
problems that I can't find solutions to in the documentation. Any help
would be much appreciated - even just pointers of what to read and where
or links to see others config files etc.
My mart install can be accessed at
http://130.239.72.85:9002/biomart/martview
1) I have uploaded sequence data for my genome (one 'column' for CDS and
one for protein). Using MartEditor, how do I specify that I want this
exported using the FASTA formatter? Also, how do I control what goes in
the header? Using XML examples with WebExample.pl works but only if the
sequence is the first attribute in the list.
2) When I use the XML generated by MartView, none of the filters I have
work. I just get a blank file returned (XML pasted below).
3) Is there any extra info I can read about importables and exportables
as I don't really understand form what is in the user manual (I'm a
biologist trying to learn all this, so a newbie to db etc.).
4) I only have filters available for the __main table, not any of the
__dm tables when I use MartEditor. Any common mistakes that can lead to
this?
5) Is it possible to view the public marts in MArtEditor so I can see
how others have things working that I want? I'm particularly interested
in GRAMENE GENES as they have everything working that I currently want.
A lot of questions I know. Help with any would be great.
Thanks
Nat Street
-- XML with non-working filters (remove filter lines and it works) --
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" formatter = "TSV" header = "0"
uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
<Dataset name = "locations" interface = "default" >
<Filter name = "strand_103" value = "+"/>
<Filter name = "lg_103" value = "LG_I"/>
<Attribute name = "gm_101" />
<Attribute name = "lg_103" />
<Attribute name = "start_103" />
<Attribute name = "stop_103" />
<Attribute name = "protid_101" />
<Attribute name = "strand_103" />
</Dataset>
</Query>
--
Nathaniel Street
Umeå Plant Science Centre
Department of Plant Physiology
University of Umeå
SE-901 87 Umeå
SWEDEN
email: [EMAIL PROTECTED]
tel: +46-90-786 5477
fax: +46-90-786 6676
