Not quite .. Here is a excerpt of my code. Function writeFASTA won't work even if the connection is opened (as the write function works) and the list variable has been generated according to the syntax you showed me. }else if (substr(buf,1,4) == "ENSG") { #ENSEMBL_GENE_ID KEYWORD gene.map <- getBM (attributes=c("hgnc_symbol","ensembl_gene_id","e nsembl_transcript_id"), filters = "ensembl_gene_id", values =buf, mart=hmart) cat("\n",miRNA.rec ,"\n") cat("\n",buf,"\n") show(gene.map) if (nrow(gene.map) == 0) next gene.id <- paste(gene.map[1,"hgnc_symbol"], "|", buf,sep="") gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id", seqType="3utr", mart=hmart) show(gene.seq) if (nrow(gene.seq >0)) { if (!file.exists(filname)) { zz <- file (filname,"w") write(miRNA.rec, zz, append = FALSE) write(miRNA.seq,zz, append = TRUE) } for (i in 1: nrow (gene.seq)) { write ("\n", zz, append = TRUE) geneDesc <- paste (">",gene.id, "|", gene.map[i,"ensembl_transcript_id"], sep="") geneSeq <- gene.seq[i,"3utr"] gene.string <- list(desc=geneDesc, seq=geneSeq) writeFASTA (gene.string, zz) } } } Here is the response that I cannot understand: > library(biomaRt) > source(file.choose()) Checking attributes ... ok Checking filters ... ok >hsa-miR-23a ENSG00000114315 hgnc_symbol ensembl_gene_id ensembl_transcript_id 1 HES1 ENSG00000114315 ENST00000232424 3utr 1 GGGGGCTCAGGCCACCCCTCCTCCTAAACTCCCCAACCCACCTCTCTTCCCTCCGGACTCTAAACAGG AACTTGAATACTGGGAGAGAAGAGGACTTTTTTGATTAAGTGGTTACTTTGTGTTTTTTTAATTTCTAAG AAGTTACTTTTTGTAGAGAGAGCTGTATTAAGTGACTGACCATGCACTATATTTGTATATATTTTATATG TTCATATTGGATTGCGCCTTTGTATTATAAAAGCTCAGATGACATTTCGTTTTTTACACGAGATTTCTTT TTTATGTGATGCCAAAGATGTTTGAAAATGCTCTTAAAATATCTTCCTTTGGGGAAGTTTATTTGAGAAA AT ensembl_transcript_id 1 ENST00000232424 Error in rec$desc : $ operator is invalid for atomic vectors > gene.string $desc [1] ">HES1|ENSG00000114315|ENST00000232424" $seq [1] "GGGGGCTCAGGCCACCCCTCCTCCTAAACTCCCCAACCCACCTCTCTTCCCTCCGGACTCTAAAC AGGAACTTGAATACTGGGAGAGAAGAGGACTTTTTTGATTAAGTGGTTACTTTGTGTTTTTTTAATTTCT AAGAAGTTACTTTTTGTAGAGAGAGCTGTATTAAGTGACTGACCATGCACTATATTTGTATATATTTTAT ATGTTCATATTGGATTGCGCCTTTGTATTATAAAAGCTCAGATGACATTTCGTTTTTTACACGAGATTTC TTTTTTATGTGATGCCAAAGATGTTTGAAAATGCTCTTAAAATATCTTCCTTTGGGGAAGTTTATTTGAG AAAAT" > writeFASTA (gene.string, zz) Error in rec$desc : $ operator is invalid for atomic vectors > -----Messaggio originale----- Da: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Inviato: gio 16/07/2009 17.43 A: mauede@alice.it Cc: bioconductor List Oggetto: Re: [BioC] R: how to use writeFASTA in modality "append" Hi, > I have the 3UTR sequence and the description in separated variables. > How can I generate a list with the two elements $seq and $desc as > expected by writeFASTA ? Let's say your var names that hold the data are: seqs and descs: fasta.list <- lapply(seq(seqs), function (i) list(seq=seqs[[i]], desc=descs[[i]])) I think that should work, no? -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact tutti i telefonini TIM! [[alternative HTML version deleted]]