> 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...
Of course, but then you miss all the flexibility that biomart gives. For instance you can filter on chromomsomes, specific regions, or IDs... and you even can select a second dataset (like ensembl gene human), and build a more complex query with xref filtering, and so on.... It all depends what you want to do with it... If you just want to dump data, well you still can do it, and the gzip output + the email notification is the best option. It dumps the data on our servers, and send you an email with a link when completed - you then "just" have to download it. hope this helps, Benoit > > > > 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 >
