Hi, On Wed, Sep 22, 2010 at 10:51 AM, Andrew Yee <[email protected]> wrote: > Is there a limit to the number of characters in a line for > read.DNAStringSet()? <snip> >> bar <- read.DNAStringSet(filepath='~/sandbox/foo.fasta', format='fasta') > Error in .read.fasta.in.XStringSet(filepath, set.names, elementType, lkup) : > reading FASTA file : cannot read line 2, line is too long
Apparently so :-) Assuming your on a *nix-type machine, you can use the `fold` command (from the terminal) to pretty easily fix your problem ... you would have to assume a maxlength for your header(?) lines (the ones in your fasta file that start with ">"). Since you've already shown that the read.DNAStringSet function can handle line lengths of 2000, maybe you can use that (or some smaller number), if you like. >From terminal: $ fold -w 2000 foo.fasta > foo.folded.fasta Then fire up R and do you reading as usual. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
