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
