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
