Create target/decoy database

Description

This script creates a target/decoy database from a set of input FASTA databases.

Input files

• at least 1 database file (.fa | .faa | .fas | .fasta)

Output files

• Target/decoy database (target-decoy.fasta)

Context

Parameters

Target-decoy method

Specify how decoys should be created.

Choices: shuffle protein, reverse protein (default), shuffle peptide

Decoy keep start

Specify how many amino acids from the start of a sequence should be left untouched when creating a decoy entry.

Default: 0

Decoy keep end

Specify how many amino acids from the end of a sequence should be left untouched when creating a decoy entry.

Default: 1

Target entry prefix

This will be prepended to every target entry during target/decoy generation.

Default: __td__target_

Decoy entry prefix

This will be prepended to every decoy entry during target/decoy generation.

Default: __td__decoy_

Amount of decoys per target

Specify how many decoys should be generated for every target.

Default: 1

Source code

decoyfasta.rb, decoyfasta.yaml (GitHub)