SpectraST_Decoy_Fasta_Generation

A small python script that generates a fasta file with correctly annotated decoys from spectraST's decoy-generation log file.

Installation

• a working python installation (~= 3.5) is required
• ensure that the packages fuzzywuzzy and biopython are available on you computer
• download the file SpectraST_DECOY_Fasta.py

Application

• open a comand window and navigate to the folder where SpectraST_DECOY_Fasta.py is stored
• type
  SpectraST_DECOY_Fasta.py -f path\to\fasta_file\fasta.fasta -l path\to\decoy_generation_log_file\Decoy_generation_log.txt -o \path\to\outfile\out_basename
  This comand will load the log file of the decoy generation and create a fasta file with decoy entries for all proteins present in the spectral library. Prefix all entries with your preferred decoy tag and append the entries to your target fasta file.

Options

• -f = Target-only fasta file that can be used to map the original peptides, required

• -l = Log file of the spectraST decoy generation step. For each peptide in the spectral library a line similar to
  'DECOY: Shuffle PEPTIDE to TIPEPDELK . (2 AAs added randomly.)'
  has to be present, required

• -s = String to separate newly generated peptides in the DECOY proteins, default = KRKR

• -d = Decoy string during the original database search, entries in the provided fasta file starting with this string are filtered prior mapping library peptides, default = 'Reverse'

• -o = Output file names. Files with the extension '.fasta' and '.tsv' will be generated. Caution: Will be overwritten, if existing!, required