> 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 > ---
Hi again, 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 Benoit > 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 >
