I think the way the GenomicSequence was coded for the snp sequence attribute was to add a newline character before and after the sequence. This was put in to help in the formatting I think when upstream and downstream sequence were chosen (ie) when you choose snp sequence and upstream and downstream you would get somthing like:
"upstream_seq"/n "A/G"/n "downstream_seq" If you get the data out using the FASTA formatter it all comes out nicely but I agree this all very HACKY and messes up the formatting for simple tab-separated format. The adding of new lines should have been handled in the FASTA formatter itself. We will look into this and fix on branch 0_4 and/or 0_5 upcoming release thanks for spotting it cheers Damian On Thu, 29 Jun 2006, David Withers wrote: > When I send the following query: > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE Query> > <Query virtualSchemaName="default" count="0"><Dataset > name="mmusculus_snp"><Attribute name="chr_name" /><Attribute > name="chrom_start" /><Filter name="chr_name" value="17" /><Filter > name="chrom_end" value="33527038" /><Filter name="chrom_start" > value="33518969" /></Dataset><Dataset > name="mmusculus_genomic_sequence"><Attribute name="snp" > /></Dataset><Links source="mmusculus_snp" > target="mmusculus_genomic_sequence" defaultLink="snp" /></Query> > > to http://www.biomart.org/biomart/martservice?query= the results I get > back are: > > 17 33519098 > A/G > > 17 33519176 > A/G > > etc, etc. > > So, I'm getting > > "17"/t"33519098"/t/n"A/G"/n/t > > but I was expecting > > "17"/t"33519098"/t"A/G"/t > > Are the extra new line characters correct? I currently process the query > results line by line but maybe this approach is too simplistic. > > David. > -- > David Withers > School of Computer Science, University of Manchester, > Oxford Road, Manchester, M13 9PL, UK. > Tel: +44(0)161 275 0145 >
