Hi Rochak,
apologies for the delay on this, we are a bit occupied with an internal
release. Anyways, I dont think OrderBy is broken, however lets check it.
Please edit the conf/log4perl file and replace INFO with DEBUG. Then
reconfigure, kill and restart apache. Now, once you fire a query from
MartView, you should be able to see SQL query in logs/error_log
let me know whether OrderBy appears in the SQL. Also, send us your XMLs
(these you need to send to me, mailing list would not accept files)
Best,
Syed
Rochak Neupane wrote:
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