Hello, Seems like this thread has been buried under the pile. I looked at the ensembl config from MartEditor, they have "OrderBy" set for the exons, and the output is not ordered.
OrderBy is apparently not working for them either. Is that a bug in BioMart? If I were to force a sorting method for exons by rank (or any other field), what would it involve? I imagine there would be a hidden attribute thats always selected, but it would only be displayed if exon sequences were selected? What would be a good way to go about doing this? Thanks, Rochak On Jan 21, 2010, at 4:46 PM, Rochak Neupane wrote: > Thanks Syed. As you suggested, I added the attribute name of rank in > "OrderBy" for the exon sequences exportable. > > I added exon_rank as the first attribute for the exportable's "attributes". > Then I added exon_rank in "OrderBy". > > I then exported, reconfigured, and restarted biomart. When I tried to get > exon sequences. I got the following error: > > ERROR: caught BioMart::Exception: non-BioMart die(): Can't locate object > method "error" via package "Can't call method "toSQL" on an undefined value > at /var/apache/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 503. > " (perhaps you forgot to load "Can't call method "toSQL" on an undefined > value at /var/apache/biomart-perl/lib/BioMart/Dataset/TableSet.pm line 503. > "?) at /var/apache/biomart-perl/lib/BioMart/Web.pm line 2273. > > If you repeatedly get directed to this error page, there may be a problem > with your current session parameters. To clear your session and start with a > clean slate, please click the New button below. > > Stacktrace: > Exception::Class::Base::new /var/apache/biomart-perl/cgi-bin/martview:78 > ModPerl::ROOT::ModPerl::Registry::var_apache_biomart_2dperl_cgi_2dbin_martview::handler > > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204 > (eval) > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204 > ModPerl::RegistryCooker::run > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170 > ModPerl::RegistryCooker::default_handler > /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31 > ModPerl::Registry::handler -e:0 > (eval) -e:0 > > But I figured the sequence importable for exon sequence might also need to be > updated, but it already had "pkey", which I assume corresponds to "exon_rank" > from the exportable, in OrderBy. Regardless of if I have pkey in the OrderBy > for the importable, I keep getting the same error as above. > > > Not having an "OrderBy" in the exportable seemed to be the only way to avoid > the error. There was no difference in behavior with or without the pkey > OrderBy in the importable. > > > I then populated the table where rows were ordered by rank and removed any > OrderBy for importable/exportables, output was not sorted in any particular > order. > > Has anyone been able to have the exon sequences (or any other data) output > ordered? > > Thanks, > Rochak > > > On Jan 20, 2010, at 5:51 PM, Syed Haider wrote: > >> Hi Rochak, >> >> In marteditor where you declare the exportable for exon sequences, you will >> see OrderBy property. type in the attribute name of rank. Export, >> reconfigure and restart. Hopefully that would do the job. If that doesnt >> work, try populating the database in a way that rows are ordered by rank. >> >> Best, >> Syed >> >> Rochak Neupane wrote: >>> Hello, Is it possible to have BioMart display exon sequences in the order >>> of exon rank in transcript? Right now the sequences are displayed in no >>> particular order. Below is an example of exon sequences from Danio rerio. >>> Last field on the header is the exon rank. >>>> ENSDARG00000079210|ENSDART00000114541|4 >>> TAATAAAAAAAATATTTATTACAGCTCAGAACAATGTTTTTTTTTCCTGTTTTATTTGTC >>> TGTTTATAGGCAAGAAATTATGTAATAAG >>>> ENSDARG00000079210|ENSDART00000114541|1 >>> CTGGACATGGCATTAAATTCAGTTGATGATCAGTATAAGGGATGTACCAAAAAAATGGCA >>> GATCTGGTGAAAACAAAATATCTGCCGAAGGAACTCAATAACTCTAAATCGTTCAAGGAA >>> GCTTGGAAAGTGGCTGAAAGATCTTTTAAGAAGCCAGAAAATAACTTGACAAATAATCAT >>> TCAATTGCCATCTATCTGTACACTGGGTTAAAACTGTTTCGTGATTTCAATAATGCCACT >>> CATCATGGCAGGCAAAACTACACAAATGAGAAATACGACTGGTATTCACTTCACTTCCTG >>> TTAACAGAGGCCTTACAGATTCTGAAAACAGCACAAAATAGATGCTTTGATACTTTTCGT >>> GGTACAAAG >>>> ENSDARG00000079210|ENSDART00000114541|3 >>> CACTGTTCGTTTTGGCTCATTTGCATCTTCCTCTTATATTCGTAACAAAGCAATGTTTTT >>> TGGAAGTGTGTCTTGTTTTGAGATTCACACTTGTGCAGGTGCTGATATTACTGATTATTC >>> CATGCTTGATCGTGAGAAAGAGGTGTTGATTCCTCCATATGAGACGTTTAGAGTCACTGA >>> AACCAAGACAA >>>> ENSDARG00000079210|ENSDART00000114541|2 >>> AATAGATGCTTTGATACTTTTCGTGGTACAAA >>> Is it something that is configurable in MartEditor? Thanks, >>> Rochak >
