> > On 24 Apr 2007, at 17:34, Syed Haider wrote: > >> Hi Max >> Correct, It should not return nucleotide sequence. >> cc'ing to Benoit, who is expert on 'Compara Marts' and he would be back >> with his findings. I am not sure about Martshell, I'll get back to you >> when I find this out. >> > > Hi Max, > I don't think you would be able to use MShell with compara mart > sequence. > This code is a bit out of date and at the moment it only supports a > standard 'genomic' types
Hi Max, I am not sure if martshell can handle unconventional data type like the compara_mart one. The key is the name of the formater you are using in martshell. You have to use these formatters _only_ (MAF, MFA, AXT, AXTPLUS). As I can see in you previous mail you have been using 'fasta' as format output, and that is the reason why you are getting unaligned sequences, plus probably the cigar lines. The 4 formatters (MAF, MFA, AXT, AXTPLUS) receive the raw sequences, and cigar lines and then proccess the sequences on the fly to produce the alignments. So try with MAF formatter, and see what happen - if it does not work, that means that probably martshell doesn't support compara_mart data. Hope this helps Benoit > > a. > > >> Cheers >> Syed >> >> >> On Tue, 2007-04-24 at 17:23 +0100, Maximilian Haeussler wrote: >>> Warning: this query would return ~665MB of data :) >>> >>> But I just wanted the peptide alignments, not 665 MB of strange >>> nucleotides... :-) >>> Well I think there is a problem with the martview output. Compare it >>> with the website martivew output (compara homology, human, ciona, >>> orthologs, features=alignments, no filter): >>> The output should be 15 MB and not genomic sequence... or maybe there >>> is something else that I don't know about the XML-parameters... >>> >>> Is there a way to do this with martshell? >>> >>> cheers, >>> Max >>> >>> >> -- >> ====================================== >> Syed Haider. >> EMBL-European Bioinformatics Institute >> Wellcome Trust Genome Campus, Hinxton, >> Cambridge CB10 1SD, UK. >> ====================================== >> > > > ------------------------------------------------------------------------ > ------- > Arek Kasprzyk > EMBL-European Bioinformatics Institute. > Wellcome Trust Genome Campus, Hinxton, > Cambridge CB10 1SD, UK. > Tel: +44-(0)1223-494606 > Fax: +44-(0)1223-494468 > ------------------------------------------------------------------------ > ------- > > >
