Changelog

Version 0.5.0 (04.2017)

  1. New branch: upapa_v3. This branch will soon be merged into the master after rigid testing and evaluation.
  2. New improved peptide mapper version in terms of RAM usage and speed. Peptide mapping is now a standalone unode. Classes for mapping can be imported from anywhere from the undoe. Input for standalone node is a not-unified csv file. Branch: upapa_v3
  3. Unify csv is now placed after the upeptide_mapper node if a database search engine (e.g. OMSSA, X!Tandem etc.) is used. Branch: upapa_v3
  4. Unify csv was adjusted to meet the new requirements of the separated peptide mapping node. Please also note, that the default behaviour of remapping amino acid ‘U’ to ‘C’ is not longer performed.
  5. Unify csv now reports if the peptide fulfills the enzyme cleavage parameters, like number of missed cleavages and if the C and N terminus is correct. Column name: ‘Complies search criteria’
  6. Test script update
  7. Documentation update
  8. Implementation of a customizable SVM for PSM post-processing
  9. Smaller fixes and improvements (please check git log)

Version 0.4.0rc1 (05.2016)

  1. included a upeptide_mapper for fast peptide to sequence mapping.
  2. renamed engine folder to wrappers
  3. combined all files from the kb folder into one single file, uparams.py which is parsed during unode initialization. Advantage is to see all params grouped together.
  4. Added more information to the unique parameters, such as description and default value types.
  5. Included script to auto-generate documentation from uparams file.
  6. Updated documentation to reflect the changes above.

Version 0.3.4 (02.2016)

  1. Implementation of de novo search engines: Novor, PepNovo
  2. X!Tandem version Vengeance included