fasta-dinucleotide-shuffle [options]
fasta-dinucleotide-shuffle-py3 [options]
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-shuffle for Python 2.7 and
fasta-dinucleotide-shuffle-py3 for 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.
| Option | Parameter | Description | Default Behavior |
|---|---|---|---|
| General Options | |||
| -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. |