Hi Max
Try the fasta in uppercase , should work that way.
Cheers
Syed
On Wed, 2007-04-25 at 10:09 +0100, Maximilian Haeussler wrote:
> Hi martguys & Benoit,
>
> thanks for your quick feedback!
>
>
> In my previous mail I thought you wanted whole genome pairwise
> alignments.
> But what I have explained also apply to the homologues, you
> have to use
> the right formatter, which is in that case FASTAA
> I had tried (weird guesswork) "set format=fastaa" in martshell.sh and
> that didn't work either. OK, let's forget about martshell. It seems
> martshell doesn't have an advantage over wget+XML-file.
> (BTW I wonder why martshell & company exist? Is it used by anyone? )
>
> So...how can I set the formatter in the XML file? (not documented, the
> documentation says that the valid parameters could be found "elsewhere
> in this document".) I tried adding a "formatter" attribute with the
> value "fastaa"... that gives me :
>
> Query ERROR: caught BioMart::Exception: could not load module
> BioMart::Formatter::fastaa: Can't locate BioMart/Formatt
> er/fastaa.pm in @INC
>
> thanks again,
> cheers
> Max
--
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Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
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