Hi Steve, just in case you have to change J for X in several fasta files, several times, this bash script does the job:
find -type f -name '*.fasta' -print0 | xargs --null perl -pi -e 's/J/X/' Hope it helps, Best On Fri, Mar 13, 2009 at 11:26 AM, Peter Rice <[email protected]> wrote: > Steve Taylor wrote: >> >> Thanks Peter. >> >> Nice detective work. I wonder if anybody in NCBI/RefSeq is reading this? >> This is where the source is from...I wonder how blast indexing handles not >> having a > for example? > > There was a '>' ... my mailer uses it for quoting so it got converted to > '>' but the file was OK. It was only the 'J' in the sequnece that broke > things. > > Peter > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss > -- Andrés Pinzón http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
