It looks like Biostrings function "writeFASTA" overwrites the output file at each run. It seems it does not support the "append" parameter. I have to generate one big file gathering a miRNA identifier and relative sequence followd by a variable number of dara records pertaining such a miRNA target genes transcription. Each record is made up of a 3'utr identifier <hgnc_id>.<ensembl_id>.<transript_id> followed by the relative 3'UTR sequence. I hoped I could use writeFASTA but it does not allow me to append sequences to the same output file. Any suggestion is more than welcome. Thank you in advance, Maura .html?pmk=footer> [[alternative HTML version deleted]]

Hi, You could try to open the file first, call the function "writeFASTA" many times using the same file as output and then close it. Something like this: fasta.file <- file("my.fasta", "w") [ some code...] writeFASTA(fasta.obj, file = fasta.file) [ more code...] writeFASTA(another.fasta.obj, file = fasta.file) [ final code...] writeFASTA(yet.another.fasta.obj, file = fasta.file) close(fasta.file) I tried it here and it worked. Alvaro. -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of mauede@alice.it Sent: Thursday, July 16, 2009 3:40 PM To: Bioconductor List Cc: r-help at stat.math.ethz.ch Subject: [BioC] how to use writeFASTA in modality "append" It looks like Biostrings function "writeFASTA" overwrites the output file at each run. It seems it does not support the "append" parameter. I have to generate one big file gathering a miRNA identifier and relative sequence followd by a variable number of dara records pertaining such a miRNA target genes transcription. Each record is made up of a 3'utr identifier <hgnc_id>.<ensembl_id>.<transript_id> followed by the relative 3'UTR sequence. I hoped I could use writeFASTA but it does not allow me to append sequences to the same output file. Any suggestion is more than welcome. Thank you in advance, Maura .html?pmk=footer> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Maura, I've added an 'append' argument to the writeFASTA() function. This is available in the latest Biostrings release (2.12.8) and devel (2.13.25). Both should propagate to our public repositories in the next 24 hours. Please update your installation by following the instructions here: http://bioconductor.org/docs/install/ Cheers, H. Quoting mauede at alice.it: > It looks like Biostrings function "writeFASTA" overwrites the output > file at each run. > It seems it does not support the "append" parameter. > > I have to generate one big file gathering a miRNA identifier and > relative sequence followd by a variable number of dara records > pertaining such a miRNA target genes transcription. > Each record is made up of a 3'utr identifier > <hgnc_id>.<ensembl_id>.<transript_id> > followed by the relative 3'UTR sequence. > > I hoped I could use writeFASTA but it does not allow me to append > sequences to the same output file. > Any suggestion is more than welcome. > > Thank you in advance, > Maura > > > > .html?pmk=footer> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >