Hi Nathaniel,
please scroll down to see how you can address these problems,
Nathaniel Street wrote:
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.
Firstly, I would recommend you to look at ensembl mart and sequence
mart, which are publicly available. Connect through MartEditor using the
credentials:
databaseType: mysql
host: martdb.ensembl.org
port: 5316
use anonymous
pass: <leave it empty>
database & schema: ensembl_mart_50 OR sequence_mart_50
With ensembl, the sequence itself comes from sequence_mart_50 and the
coordinates are used from ensembl_mart_50. This is all handled by
Exportables and Importables. If you have CDS or Proteins already
processed and stored in once column, then I am afraid you see the right
behaviour from software point of view that sequence should be the first
attribute in user selection. If you want to hack this based on the name
of the attribute e.g if (attName == CDS), feel free to do this in
lib
<http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/lib/?root=BioMart#dirlist>
/ BioMart
<http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/lib/BioMart/?root=BioMart#dirlist>
/ Formatter
<http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/biomart-perl/lib/BioMart/Formatter/?root=BioMart#dirlist>
/ FASTA.pm
You can also write a custom formatter, and leave it in this directory.
That will be your own formatter.
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).
How are you using the MartView generated XML where the filters ar'nt
working. Please send me your client.
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.).
Ensembl mart example would help you on this. Exp/Imps are matching pairs
which establish linking between two local or remote datasets which may
belong to same or different marts. Let me know if you need more details
on this.
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?
sorry, are you getting some errors around this issue ? unless its not
point 2 you mentioned above.
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.
Yes certainly possible with MartEditor. With Gramene, I am not sure if
you can. Gramene is derived from Ensembl data-model anyways. You can
look at ensembl. cc'ing to Will and Richard, between them, they manage
Gramene.
A lot of questions I know. Help with any would be great.
Hope this helps.
Cheers
Syed
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>
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
