I just committed a fix to the latest code. We will be releasing this code
as 0.6 on the central server in the next day or so should be fine then
On Wed, 13 Jun 2007, Damian Smedley wrote:
Hi,
definitely seems we have +/-1 error somewhere in our code - I will
investigate
Thanks
Damian
On Wed, 13 Jun 2007, Bogdan wrote:
Dear all,
if I issue a simple query like this:
<Query virtualSchemaName = "default" header = "0" count = ""
softwareVersion = "0.5" >
<Dataset name = "rnorvegicus_gene_ensembl" interface = "default" >
<Attribute name = "gene_stable_id" />
<Attribute name = "transcript_chrom_strand" />
<Attribute name = "5utr" />
<Filter name = "transcript_status" value = "KNOWN"/>
<Filter name = "ensembl_gene_id" value =
"ENSRNOG00000004258,ENSRNOG00000014029"/>
</Dataset>
</Query>
and align the resulting sequence with a result from this query:
<Query virtualSchemaName = "default" header = "0" count = ""
softwareVersion = "0.5" >
<Dataset name = "rnorvegicus_gene_ensembl" interface = "default" >
<Attribute name = "gene_stable_id" />
<Attribute name = "transcript_chrom_strand" />
<Attribute name = "5utr" />
<Filter name = "upstream_flank" value = "1000"/>
<Filter name = "transcript_status" value = "KNOWN"/>
<Filter name = "ensembl_gene_id" value =
"ENSRNOG00000004258,ENSRNOG00000014029"/>
</Dataset>
</Query>
then for the ENSRNOG00000004258 the first common base is in position
1001 (from the start of the longer sequence), and for the
ENSRNOG00000014029 the first common base is in position 1000.
The case-important difference between the two genes is strand:
positive for 14029 and negative for 4258. This behaviour isn't unique
to these two genes - seen the same for ~6 other genes.
Is this a minor inconsistency, or a feature?
Will appreciate your clarification,
