For a given primer sequence with degenerate bases in IUPAC notation this script prints out sequences for all the permutations that are possible.
This script requires BioRuby.
Pipe a FASTA formatted file into this script, and this script will output a new FASTA file with the new sequences on STDOUT.
For each FASTA entry ID, the new entry IDs for the permuted sequences will be appended with _1, _2, etc. Note that the script does not check for entry ID collisions, e.g. if you used the same entry ID twice.