Remove line breaks in a FASTA file

Question

I have a fasta file where the sequences are broken up with newlines. I\'d like to remove the newlines. Here\'s an example of my file:

>accession1
ATGGCC         


        

Answer 1

You might be interested in bioawk, it is an adapted version of awk which is tuned to process fasta files

bioawk -c fastx '{ gsub(/\n/,"",seq); print ">"$name; print $seq }' file.fasta

Note: BioAwk is based on Brian Kernighan's awk which is documented in "The AWK Programming Language", by Al Aho, Brian Kernighan, and Peter Weinberger (Addison-Wesley, 1988, ISBN 0-201-07981-X) . I'm not sure if this version is compatible with POSIX.