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