The program fasta-dinucleotide-shuffle creates a shuffled version of a FASTA file of nucleotide sequences (other alphabets may be specified). The letters in each sequence in the input file are shuffled in such a way that dinucleotide frequencies are exactly preserved. Any alias symbols are converted to their core symbol before shuffling.
Note that the other shuffling program provided with the MEME Suite, fasta-shuffle-letters, supports all the features that fasta-dinucleotide-shuffle has and runs faster so it should be used in preference.Two different versions of fasta-dinucleotide-shuffle are provided:
fasta-dinucleotide-shufflefor Python 2.7 and
fasta-dinucleotide-shuffle-py3for Python 3.x. The random number generator has changed between Python 2.7 and Python 3.x, so results between the two verisons may differ.
Sequences in FASTA format from a file.
Writes a FASTA format file to standard output.
|-f||filename||Name of input file (required).||None.|
|-t||tag||The letters in tag are appended to the FASTA identifier of each shuffled sequence.||Each shuffled sequence has the same name as the original.|
|-s||seed||Use seed as the starting seed for the random number generator.||1|
|-c||n||Make n shuffled copies of each original sequence.||Make 1 shuffled copy.|
|-a||filename||Provide the alphabet definition to use for non-DNA alphabets. Sequences will be verified to be in the given alphabet.||Use the standard DNA alphabet.|