Skip to content

A Python script to convert the spectral library in BLIB format (.blib) from either Skyline or BiblioSpec to readable library format (OpenSwath or Spectronaut libraries)

License

Notifications You must be signed in to change notification settings

chinmayaNK22/Blib2OpenSwath

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

52 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Blib2OpenSwath

A Python script to convert the spectral library in BLIB format (.blib) from either Skyline or BiblioSpec to readable library format (OpenSwath or Spectronaut tsv format)

Installation of requirements

>pip install -r requirements.txt

Usage

>python blib2openswath.py -h

usage: blib2openswath.py [-h] [--infile -i [-i ...]] [--fasta -f [-f ...]] [--tol -t [-t ...]] [--mz_type -m [-m ...]]

Blib2OpenSwath: Convert spectral library from BLIB (Skyline) to OpenSwath format

optional arguments:
  -h, --help            show this help message and exit
  --infile -i [-i ...]  The input spectral library file in BLIB format either from Skyline or BiblioSpec output
  --fasta -f [-f ...]   Proteome database in fasta format for mapping peptides sequences
  --tol -t [-t ...]     Library match tolerance in dalton (Da) for fragment m/z annotation (INFO: The tolerance of 0.5 Da and 0.05 Da was set as default)
  --mz_type -m [-m ...] Specify the type of fragment m/z values present in the input spectral library (Ex: "average" or "mono")
  --lib_fmt -l [-l ...] Specify the spectra library format (Ex: "openswath" or "spectronaut")
  --fmt -o [-o ...]     Specify the output spectra library file format (Ex: "tsv" or "csv")

Example

>python blib2openswath.py --infile data\library\Spectral_library.blib --fasta data\database\sequence.fasta --tol 0.02 --mz_type mono 

Contact

For more information, post an issue or send an email to [email protected]

About

A Python script to convert the spectral library in BLIB format (.blib) from either Skyline or BiblioSpec to readable library format (OpenSwath or Spectronaut libraries)

Topics

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages