v0.8.0

Added

• io.timscore: Add support for TIMScore Parquet files.

Fixed

• Fixed _csv.Error: field larger than field limit (131072) for very large fields when reading CSV-based PSM files.
• Pinned Pyteomics version to avoid pickling issues in multithreading (to be investigated)

---

Full Changelog: v0.7.4...v0.8.0

v0.7.4

Added

• Peptidoform: Support adding and applying global terminal modifications. For now using a
  workaround while waiting for official support and an implementation in Pyteomics. See
  HUPO-PSI/ProForma#6.

Full Changelog: v0.7.3...v0.7.4

v0.7.3

Changed

• io.xtandem: Parse double mass modifications as double modification instead of merging and summing mass shifts into a single modification.
• io.xtandem: Avoid float formatting issues when parsing modification mass label.
• io.xtandem: Parse all proteins into protein_list instead of only the first one.
• io.tsv: Log error instead of raising exception when a TSV row cannot be parsed.

Full Changelog: v0.7.2...v0.7.3

v0.7.2

Fixed

• io.xtandem: Fixed bug when extracting run name (introduced in v0.7.0) (#63)

v0.7.1

Added

• Tests: Added tests for _format_number_as_string function
• Tests: Added more test cases for peptidoform.rename_modifications for mass modifications
• io.xtandem: To parse run value, fall back to PSM file name if run name cannot be parsed from label field

Fixed

• peptidoform.rename_modifications: Fixed mapping of negative mass modifications
• io.xtandem: Fixed regular expression to parse run value fom XML label field
• io.idxml: Fix handling multiple types in rescoring_features when writing (fixes #60)

Full Changelog: v0.7.0...v0.7.1

v0.7.0

Added

• io.idxml: Write support for idXML files, including merging an existing idXML with a PSMList 🎉
• io.xtandem: New argument score_key to select which score to parse as PSM.score.
• io.xtandem: Parse run name from X!Tandem PSM files
• Docs: Add intersphinx links to other package documentation pages.

Changed

• io.idxml: Use pyOpenMS instead of Pyteomics for reading idXML (~5x faster⚡)

Fixed

• Fix reading of pepXML files without RT
• Fixed Black formatting throughout project

v0.6.1

Fixed

• io.pepxml: Fix reading pepXML files without retention time information.

v0.6.0

Added

• io: Added new io.pepxml reader

Fixed

• Docs: Add ionbot to README.rst, fix order in API docs

v0.5.0

Added

• Peptidoform: Added support for iter() and len() methods
• Peptidoform: Added support for initialization from a pyteomics.proforma.ProForma object
• PSM: Add precursor_mz_error property
• PSMList: Added support for append() and extend() methods.
• io: Added new io.ionbot reader
• io: Added support for Proteome Discoverer MSF files
• io.mzid: Parse inverse reduced ion mobility from mzid files (e.g. from PEAKS)
• io.mzid: Add support for user to define custom score key
• io.mzid: Add Proteome Discoverer Delta Score to known scores (with spaces, no colons)
• io.mzid: Allow inconsistent presence of score in PSMs in a single mzid file

Changed

• PSM: Values of the rescoring_features dictionary are now coerced to floats
• io: Raise PSMUtilsIOException when passed filetype is not known
• io: Make io reader read_file method inheritable (code cleanup)
• io.mzid: Throw warning when no known score can be parsed from mzid file instead of error
• io.mzid: Move spectrum level parsing of rt and ion mobility to function
• io.mzid: Give PeptideShaker PSM score priority over other potential search engine scores (required for correct PeptideShaker mzid parsing)
• io.percolator: Add option to write PSMScore and ChargeN as features to PIN file. Default is now False.
• Formatting: Increase max line length to 99 (code formatting)

Fixed

• PSMList: Fix issue where psm_list["protein_list"] resulted in a Numpy error due to the inconsistent shape of the lists.
• io.tsv: Throw more descriptive PSMUtilsIOException when handeling tsv errors
• io.msamanda: Fix support for N/C-terminal modifications
• io.Percolator.PercolatorTabWriter: Allow rescoring features that are not in feature_names (extrasaction is now specified in DictWriter)
• Use raw strings for escape characters where needed
• Fix compatibility with sqlalchemy 2.0 (move of declarative_base)
• online: Remove useless == True
• docs: Set newer build>os configuration for readthedocs.org
• CI: Upgrade Github action versions

v0.4.1

Changelog

Fixed

• PSMList: Revert comparison operator change from v0.4.0 that results in broken calculate_qvalues() method (E711; Numpy array, not singleton)

Full Changelog: v0.4.0...v0.4.1