Version 0.6.9 (05.2021)

  1. reformat with black
  2. allow multiple modifications at the same site
  3. minor bug fixes and update dependencies

Version 0.6.8 (12.2020)

  1. Simplified the isntallation of third-party engines

Version 0.6.7 (11.2020)

  1. Implemented pNovo 3.1.3
  2. Implemented pGlyco 2.2.2
  3. Implemented Percolator 3.4.0
  4. Implemented PTM-Shepherd 0.3.5
  5. Implemented TagGraph 1.8.0
  6. Implemented latest version of MODa (v1.62), MSAmanda (version, MSFragger (20190628, 2.3, 3.0), DeepNovo (PointNovo)

*. Implemented glycopeptide search functionality for MSFragger 3.0 #. Implemented MS-GF+ v2019.07.03 and included enzymes.txt for more and customized options #. PSM defining columns for sanitize_csv and combine_PEP are now

specified though uparams
  1. Added advanced protein digest functionality (to ucore) adapted from Pyteomics’ cleave function
  2. venndiagram_1_1_0 can now also print percentages for each field
  3. Added signal_to_noise_threshold option for mzml2mgf conversion
  4. internal changes to the mapping of styles and uparams in umapmaster

Version 0.6.6 (03.2020)

  1. (and pip) installs resources now
  2. Added Percolator 3.4
  3. Dropped pymzml v0.7.x support - mzml2mgf v2.0.0 is default. If pymzml v.07 is required change default mzml2mgf converter back to 1.0.0
  4. Dropped Python 3.4 support

Version 0.6.5 (05.2019)

  1. Added ThermoRawFileParser for conversion of .raw to .mzML/.mgf
  2. Added pGlyco 2.2.0, including pParse 2.0 and pGlycoFDR 2.2.0
  3. Added DeepNovo 0.0.1 (so far only search_denovo functionality)
  4. Added latest version of MSGF+ (version 2019.04.18) and MSFragger (version 20190222)

Version 0.6.4 (05.2019)

  1. Fixed bug in unify csv where N-terminal mods were not assigned the correct position
  2. Added possibility to write result groups of venndiagram to csv
  3. Use setuptools instead of distutils in
  4. Allowed installation via PyPI

Version 0.6.3 (03.2019)

  1. Added Percolator 3.2, including the options to infer protein PEP and FDR
  2. Added latest versions of MSGF+ (version 2019.01.22) and MSAmanda (version and Novor (version 1.05)
  3. Added support for conversion of mzML files originating from .wiff files based on the id_dict property in the latest pymzML version (2.1.0)
  4. Some minor bugfixes and improvements (check git log for details)

Version 0.6.2 (09.2018)

  1. MSFragger version 20171106 was implemented
  2. MODa v1.61 was implemented
  3. PIPI version 1.4.5 replaced PIPI 1.3 due to compatibility issues with PIPI 1.3
  4. PIPI version 1.4.6 implemented (thanks Fengchao)
  5. Added latest versions of MSGF+ (version 2018.06.28 and 2018.09.12) and new python mzid to csv converte msgfplus2csv_py_v1_0_0
  6. Macot wrapper and converter was implemented to allow downstream processing of Mascot results
  7. Some minor bugfixes and added functionality (check git log for details)

Version 0.6.1 (03.2018)

  1. Improved compaitibility to pymzML generation 2 and splitted up the mzML to mgf converter in version 1.0.0 (pymzML 0.7.9) and 2.0.0 (pymzML 2.0.2). The version of installed pymzML is now automatically determined and the corresponding converter version is used.
  2. Added latest versions of MSGF+ (version 2018.01.20) and the corresponding C based mzidentML converter (version 1.2.0 and 1.2.1)
  3. Several new engine versions were made avaliable via the install_resources script.
  4. Some general code cleanup was done

Version 0.6.0 (01.2018)

  1. Restructuring of engine classes. SEARCH_ENGINE(s) are now devided into * CROSS_LINK_SEARCH_ENGINE(s) * DE_NOVO_SEARCH_ENGINE(s) * PROTEIN_DATABASE_SEARCH_ENGINE(s) * SPECTRAL_LIBRARY_SEARCH_ENGINE(s) The META_INFO of corresponding engines has been changed accordingly. Furthermore, CONVERTER(s) have been split into CONVERTER(s) and MISC_ENGINE(s)
  2. Restructuring of UController functions. Unified functions for all engines of one engine class (Converter, Search_Engines, Validation_Engines, etc) are now available. Function names for each engine class are stored in ukb.ENGINE_TYPES and ukb.UCONTROLLER_FUNCTIONS
  3. has been renamed to
  4. Implemented the following open modification search engines (as protein database search engines): MSFragger, PIPI, ModA
  5. Smaller fixes and improvements (please check git log)

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, 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