# The MEME Suite

## Motif-based sequence analysis tools

## fasta-holdout-set

### Usage:

`fasta-holdout-set` [options] --p <primary sequences>

### Description

Split primary and control sequences into training and testing sets. Control sequences are generated by shuffling if not specified. Primary sequences will be centrally trimmed to a specified length if requested.

### Input

<primary sequences>

The name of a file containing the primary (positive) sequences in FASTA format. The file must contain at least two valid sequences or `fasta-holdout-set` will reject it.

### Output

`fasta-holdout-set` writes its output to files in a directory named `fasta-holdout-set_out`, which it creates if necessary. You can change the output directory using the --o or --oc options. The directory will contain:

- `train_pos.fa` - the primary training set
- `train_neg.fa` - the control training set

Unless option --hofract (see below) is given and is equal to zero the output directory will also contain:

- `test_pos.fa` - the primary testing (hold-out) set
- `test_neg.fa` - the control testing (hold-out) set

Note: All options may be preceded by a single dash (-) instead of a double dash (--) if desired.

### Options

Option | Parameter | Description | Default Behavior
--- | --- | --- | ---
Output

--n

control sequences

The name of a file containing control (negative) sequences in FASTA format. The control sequences must be in the same sequence alphabet as the primary sequences. If the average length of the control sequences is longer than that of the primary sequences, `fasta-holdout-set` trims the control sequences so that both sets have the same average length.

If you do not provide control sequences, `fasta-holdout-set` creates them by shuffling a copy of each primary sequence, using a m-order shuffle (see next option). Shuffling also preserves the positions of non-core (e.g., ambiguous) characters in each sequence to avoid artifacts.

--order

m

If you do not provide control sequences, `fasta-holdout-set` will do an an m-order shuffle of each primary sequence to to create control sequences. This preserves the frequencies of words of length m+1 in each shuffled sequence. Unless you specify a background model file (see --bfile, below), `fasta-holdout-set` will also estimate an m-order Markov background model from the control sequences (or the primary sequences if you do not provide control sequences). `fasta-holdout-set` uses the `fasta-get-markov` program with a total pseudocount of 1 to create the Markov model. m must be in the range [0,..,5].

`fasta-holdout-set` uses m=2 (DNA and RNA), and m=0 (Protein and Custom alphabets).

--hofract

hofract

The fraction of the primary and control sequences that `fasta-holdout-set` will randomly select and place in the hold-out set output files.
Note: If a value of 0 is specified, no hold-out set output files are created and the training set files will contain all the original sequences.
Note: If a hold-out set would contain fewer than 5 sequences, `fasta-holdout-set` creates an empty output file.

`fasta-holdout-set` places 0.1 (10%) of the primary and control sequences in the hold-out set output files.

--seed | seed | Random seed for shuffling and sampling the hold-out set sequences (see above). | `fasta-holdout-set` uses a random seed of 0.
--ccut | size | Trim the primary sequences to their central region of size characters before creating the control sequences and before splitting the sequences into training and testing sets. A value of 0 indicates that the primary sequences should not be trimmed. Note: If you provide control sequences they will never be trimmed. | A value of 0 is used.
--verbosity | 1|2|3|4|5 | A number that regulates the verbosity level of the output information messages. If set to 1 (quiet) then `fasta-holdout-set` will only output warning and error messages, whereas the other extreme 5 (dump) outputs lots of information intended for debugging. | The verbosity level is set to 2 (normal).