fasta-shuffle-letters [options] <sequence file> [<output file>]
The program fasta-shuffle-letters creates a shuffled version of a FASTA file. The letters in each sequence in the input file are shuffled in such a way that k-mer frequencies are exactly preserved where k is by default 1 but may be set by the "-kmer" option.
The underlying implementation uses uShuffle.
Sequences in FASTA format from a file.
Writes a FASTA format file to the optional output file or standard output if it is left unspecified.
|-kmer||num||Shuffle the sequences so groups of num symbols appear with exactly the same frequencies. Note that in setting this number you must maintain a balance - the larger the number the more realistic the sequence will be however too large and it will not be shuffled at all! A value of 2 is used by MEME-ChIP. For values larger than 1 specifing the alphabet is highly recommended because it allows for the translation of aliases which may be important in some cases like soft-masked sequence.||A value of 1 is used which allows the shuffle to be completely random.|
|-copies||num||The number of shuffled copies to create for each sequence in the source.||A single shuffled sequence is created for each sequence in the source.|
|-dna||As if the -alph option was specified with the standard DNA alphabet as input.|
|-protein||As if the -alph option was specified with the standard protein alphabet as input.|
|-rna||As if the -alph option was specified with the standard RNA alphabet as input.|
|-alph||file||The sequences will have their symbols converted to their primary representation in the given alphabet definition. Any unknown symbols will be converted to the alphabet's wildcard.||When no alphabet is specified symbols must match exactly to be considered the same.|
|-line||num||The sequences will be output with a maximum of num symbols per line.||A line length of 100 is used.|
|-tag||text||The name of the sequence will have text appended to it.||The name of the sequence will have "_shuf" appended to it.|
|-seed||num||Set the seed of the random number generator to num.||Seed the random number generator from the computer as randomly as possible.|
|-help||Display a brief help message and exit.|