# subtract-index

## Usage:

`crux subtract-index [options] <tide index 1> <tide index 2> <output index>`

## Description:

This command takes two peptide indices, created by the tide-index command, and subtracts the second index from the first. The result is an output index that contains peptides that appear in the first index but not the second.

## Input:

- `tide index 1` – A peptide index produced using tide-index
- `tide index 2` – A second peptide index, to be subtracted from the first index.
- `output index` – A new peptide index containing all peptides that occur in thefirst index but not the second.

## Output:

The program writes files to the folder `crux-output` by default. The name of the output folder can be set by the user using the `--output-dir` option. The following files will be created:

- `subtract-index.target.txt` – a tab-delimited text file containing the target peptides.
- `subtract-index.decoy.txt` – a tab-delimited text file containing the decoy peptides.
- `subtract-index.log.txt` – a log file containing a copy of all messages that were printed to stderr.
- `subtract-index.params.txt` – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.

## Options:

- ### Input and output

  - `--mass-precision <integer>` – Set the precision for masses and m/z written to sqt and text files. Default = `4`.
  - `--output-dir <string>` – The name of the directory where output files will be created. Default = `crux-output`.
  - `--overwrite T|F` – Replace existing files if true or fail when trying to overwrite a file if false. Default = `false`.
  - `--parameter-file <string>` – A file containing parameters. See the parameter documentation page for details. Default = `<empty>`.
  - `--peptide-list T|F` – Create in the output directory a text file listing of all the peptides in the database, along with their corresponding decoy peptides, neutral masses and proteins, one per line. Default = `false`.
  - `--verbosity <integer>` – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = `30`.