Hi Maximilian In order to execute a query via terminal/shell, you need to remove
<!DOCTYPE Query> from your query, In future release we will remove it from XML button output too or rather associate a DTD instead. In the case you mentioned, the query would be wget 'http://www.biomart.org/biomart/martservice?query=<?xml version="1.0" encoding="UTF-8"?><Query virtualSchemaName = "default" header = "0" count = "" softwareVersion = " 0.5" ><Dataset name = "compara_cint_hsap_orthologs" interface = "default" ><Attribute name = "aln_peptide" /><Attribute name = "aln_genome_name" /><Attribute name = "aln_chro" /><Attribute name = "aln_gene_id" /><Attribute name = "aln_transcript_id"/></Dataset></Query>' -O temp.txt Warning: this query would return ~665MB of data :) Cheers Syed On Tue, 2007-04-24 at 16:14 +0100, Maximilian Haeussler wrote: > Hi martguys, :) > > I've continued using martshell, but I can't find a way to extract the > clustal peptide alignments from compara as faa-files. I can do it > manually using martview but I'd like to use it in a local script... is > it possible to get the alignments with martshell? > > --- > MartShell> set format=fasta; > MartShell> get aln_peptide; > Attribute aln_peptide is not found in this mart for dataset default > --- > > I've found a similar thread > http://www.mail-archive.com/[email protected]/msg00665.html and tried > to adapt your answer from it to my problem. But the following command > (pasted from martview's XML output) doesn't return anything remotely > similar to peptide alignments...looks more like a genomic sequence... > --- > wget 'http://www.biomart.org/biomart/martservice?query=<?xml > version="1.0" encoding="UTF-8"?><!DOCTYPE Que > ry><Query virtualSchemaName = "default" header = "0" count = "" > softwareVersion = " 0.5" ><Dataset name = " > compara_cint_hsap_orthologs" interface = "default" ><Attribute name = > "aln_peptide" /><Attribute name = "a > ln_genome_name" /><Attribute name = "aln_chro" /><Attribute name = > "aln_gene_id" /><Attribute name = "aln_ > transcript_id"/></Dataset></Query>' -O temp.txt > --- > > Any ideas? > > thanks a lot! > cheers, > Max -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
