mauede at alice.it
2009-Jul-17 01:16 UTC
[R] How to prpare the input data to writeFASTA ? Examples of CharacterToFASTArecords ...
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]]