Hi Johanna,
this is fixed and in cvs now. The BioMart Central Server will be updated
with changes in couple of days.
As explained earlier, the missing ranks of exons per transcript would
all appear correctly and complete. However the second level mapping
which is 'sequence type' (transcript->exon->sequenceType) will remain
ambiguous because these are not distinct per exon. You may consider
requesting exon sequence separately to retrieve 'sequence type' of each
exon for this purpose.
Thanks for your patience.
for further assistance, feel free to write back.
Cheers
syed
On Thu, 2007-07-26 at 16:47 -0700, Johanna Eddy wrote:
> If I use the MartView to obtain exon info along with the transcript sequence,
> the header is missing some of the sequence type and rank data. The query
> looks like this:
>
> my $query =
> BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
>
>
> $query->setDataset("hsapiens_gene_ensembl");
> $query->addFilter("with_refseq_dna", ["Only"]);
> $query->addFilter("chromosome_name", ["Y"]);
> $query->addAttribute("str_chrom_name");
> $query->addAttribute("gene_stable_id");
> $query->addAttribute("transcript_stable_id");
> $query->addAttribute("transcript_chrom_start");
> $query->addAttribute("transcript_chrom_end");
> $query->addAttribute("exon_stable_id_v");
> $query->addAttribute("type");
> $query->addAttribute("exon_chrom_start");
> $query->addAttribute("exon_chrom_end");
> $query->addAttribute("exon_chrom_strand");
> $query->addAttribute("rank");
> $query->addAttribute("transcript_exon_intron");
>
> And some of the results look like this:
>
> This one has 6 exon IDs, 6 exon start, 6 exon end, and 6 exon ranks, but only
> 3 types.
> >Y|ENSG00000099715|ENST00000362095|4928267|5033485|ENSE00001091626.2;ENSE00001384166.1;ENSE00000981568.3;ENSE00001494509.1;ENSE00001324247.1;ENSE00001368624.1|mixed_3utr_plus;coding;mixed_5utr_plus|5032385;5026256;4984930;4960711;4928267;4959947|5033485;5028748;4985500;4960769;4928646;4960052|1|6;5;4;3;1;2
>
> This one has 18 exon IDs, 18 exon start, 18 exon end, but only 4 exon type,
> and 15 exon ranks
> >Y|ENSG00000067048|ENST00000360160|13525413|13539845|ENSE00001402535.1;ENSE00001428977.2;ENSE00000773391.1;ENSE00001403038.1;ENSE00000773385.1;ENSE00000773394.1;ENSE00000773390.1;ENSE00000773383.1;ENSE00000862008.1;ENSE00000862007.1;ENSE00000862006.1;ENSE00000773386.1;ENSE00000773388.1;ENSE00000773384.1;ENSE00000773393.1;ENSE00000773387.1;ENSE00000773392.1;ENSE00000773389.1|5utr;mixed_3utr_plus;coding;mixed_5utr_plus|13525413;13539349;13535870;13526240;13537823;13534033;13536190;13538709;13528842;13530665;13533145;13537567;13536936;13538213;13534269;13537189;13535024;13536373|13525719;13539845;13535955;13526286;13537940;13534188;13536288;13538848;13528899;13530712;13533274;13537748;13537080;13538366;13534368;13537333;13535159;13536533|1|1;18;9;2;15;6;10;17;3;4;14;12;16;13;11
>
> Is this a bug, and can it be fixed?
>
> Thank you,
> Johanna Eddy
>
>
>
>
>
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
