sorry, please forget my last mail, just figured that the word FASTAA has to be uppercase for some reason...Benoit actually wrote it uppercase. (I know case is important in XML attributes but I usually forget it as the rest is not case-sensitive.) Thanks again, I can download the data now. cheers, Max
PS: I wonder if a plain ftp textfile download for these kinds of things (orthology assignments = csv, alignments = fastaa, sequences = fa, etc) wouldn't be easier for everyone than the rather complex mart system. Textfiles on your ftp server like Hs-Mm.pep.fastaa would be a very straightforward solution, for instance... On 25/04/07, Maximilian Haeussler <[EMAIL PROTECTED]> 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
-- Maximilian Haeussler, skype: maximilianhaeussler
