I realize function write FASTA expects a list with two items, respectively, description and sequence. However, just passing a list won't work (please, see code at the bottom of this message) I saw there is the helper function CharacterToFASTArecords(x) that presumably generates the right input data format. It would b very useful to get some example of CharacterToFASTArecords(x) usage. The on-line documentation reads: "For CharacterToFASTArecords, the (possibly named) character vector to be converted to a list of FASTA records as one returned by readFASTA" Since I have description and sequnce in separate variables ... I do not know how to use it. zz <- file (filname,"w") write(miRNA.rec, zz, append = FALSE) write(miRNA.seq,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) Thank you in advance for your help. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi, On Jul 16, 2009, at 9:16 PM, <mauede at="" alice.it=""> <mauede at="" alice.it=""> wrote: > I realize function write FASTA expects a list with two items, > respectively, description and sequence. > However, just passing a list won't work (please, see code at the > bottom of this message) Sorry ... perhaps we're not understanding your problem. Doesn't the reply I sent earlier today work? If I'm not mistaken, didn't you say that you two variables that have the description and sequence info for your data, like so? library(Biostrings) desc <- paste("gene", 1:10, " some other stuff", sep="") seqs <- replicate(10,paste(sample(c('A','C','G', 'T'), 50, replace=TRUE), collapse="")) Because this works for me: fasta.list <- lapply(1:length(desc), function(i) list(desc=desc[i], seq=seqs[i])) writeFASTA(fasta.list, 'test.fa') > I saw there is the helper function CharacterToFASTArecords(x) that > presumably generates the right input data format. > It would b very useful to get some example of > CharacterToFASTArecords(x) usage. > The on-line documentation reads: > "For CharacterToFASTArecords, the (possibly named) character vector > to be converted to a list of FASTA records as one returned by > readFASTA" > Since I have description and sequnce in separate variables ... I do > not know how to use it. That function expects the description to be in the "names" attribute of your character vector. For example, taking the same variables from above: names(seqs) <- paste("gene", 1:10, sep='') fasta.list <- CharacterToFASTArecords(seqs) > zz <- file (filname,"w") > write(miRNA.rec, zz, append = FALSE) > write(miRNA.seq,zz, append = TRUE) I don't get why you're writing something here manually if this is supposed to be your fasta file, then calling writeFASTA on it ... > # > 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) For starters, you shouldn't be pasting the ">" in the description attribute, as writeFASTA will take care of it. Assuming your seqs and descs vars are as I wrote above, just use the example as I gave it ... it'll work. -steve btw - I'm not sure cross posting to r-help is necessary, as this is BioC specific, so I removed it from the reply. -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos