CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.2.0] - 2024-11-19

Added

• ✨ io.alphadia: Read support for AlphaDIA precursors.tsv (#103 by @rodvrees)
• ✨ io.fragpipe: Read support for FragPipe psm.tsv (#103 by @rodvrees)
• ✨ io.diann: Read support for DIA-NN TSV (#103 by @rodvrees)

Changed

• 💥 psm_list: When returning a PSM property across the full PSMList (e.g. psm_list["peptidoform"]), np.fromiter is now used instead of np.array. This fixes an issue where if all peptidoforms have the same length, a 3D array of parsed sequences (amino acids and modifications) was be returned instead of an array of Peptidoform object. However, this does mean that all resulting arrays will have the object dtype instead of the previously coerced dtypes. This might lead to issues downstream. (#102)
• ➖ io.idxml: Make pyOpenMS an optional dependency, working around OpenMS/OpenMS#7600 for now. For idxml support, install psm_utils with the idxml extra dependencies. (#107 by @paretje)

Fixed

• 🐛 io.pepxml: Fix modification location and mass parsing. Position had an off-by-one error and the reported mass was the sum of the residue and modification instead of the modification alone. (fixes #100, #104)

[1.1.1] - 2024-10-01

Fixed

• io: Fix Sage filename pattern for automatic file type inference
• io.flashlfq: Fix writing PSMs without protein accession
• io.flashlfq: Fix column names Peptide Monoisotopic Mass and Protein Accession.
• io.idxml: Fix parsing if spectra file name not present #92

[1.1.0] - 2024-09-05

Added

• Peptidoform: Add modified_sequence property to return the modified sequence in ProForma format, but without charge state.
• io: Add support for reading and writing FlashLFQ generic TSV files.

[1.0.1] - 2024-08-28

Fixed

• io.percolator: Fix and improve ScanNr inferring and writing
• io.percolator: Infer style from file extension if not provided (enables dynamic style determination in, for instance, convert function).

[1.0.0] - 2024-08-14

Added

• Peptidoform: Allow comparison between a peptidoform and a peptidoform string; allow direct indexing with square brackets, which indexes or slices parsed_sequence (in #89)

Fixed

• TSV: Avoid flooding logs when reading a different file format by raising exception when three consecutive rows could not be parsed (in #88)

[0.9.1] - 2024-07-17

Fixed

• io.xtandem: Fix parsing PSMs and complete protein names in XTandem (by @julianu in #83)
• io.tsv: Fix warning formatting when parsing TSV (by @paretje in #85)
• io: Fix support for mzIdentML and pepXML files from Comet (by @paretje in #87)

[0.9.0] - 2024-05-01

Added

• io: Read and write support for writing PSMs to Apache Parquet for efficient storage of PSM lists.
• io.sage: Support for Sage results in Parquet format (new SageParquetReader, renamed SageReader to SageTSVReader).

Changed

• Upgrade Pydantic dependency to v2. The PSM spectrum_id field is now always coerced to a string.
• io.proteoscape: Use pyarrow to iteratively read from Parquet instead of first reading an entire dataframe with Pandas.
• io.sage: Update compatibility to Sage v0.14
• Remove temporary patch for caching Proforma modification resolvers (now in Pyteomics v4.7.2).

[0.8.3] - 2024-04-16

Added

• Speed up mass calculation for large datasets by caching Proforma modification resolvers. Temporary patch until implemented in Pyteomics (see levitsky/pyteomics#147).

[0.8.2] - 2024-04-05

Added

• io.proteoscape: Parse filename into PSM run field.

[0.8.1] - 2024-03-29

Added

• io.proteoscape: Allow ProteoScapeReader instantiation from Pandas DataFrame and access PSM by index.

Fixed

• Remove accidental print statement.
• io.idxml: Fixed parenthesis in type hint

Changed

• io.idxml: Filter OPENMS_DATA_PATH warnings (see compomics/ms2rescore#129 and OpenMS/OpenMS#7418)
• io.proteoscape: Rename module from TIMScore to ProteoScape.
• io.proteoscape: Use correct search engine score (x_corr_score instead of tims_score)

[0.8.0] - 2024-03-27

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)

[0.7.4] - 2024-03-18

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.

[0.7.3] - 2024-03-04

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.

[0.7.2] - 2023-11-29

Fixed

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

[0.7.1] - 2023-10-30

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)

[0.7.0] - 2023-10-25

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

[0.6.1] - 2023-10-25

Fixed

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

[0.6.0] - 2023-10-19

Added

• io: Added new io.pepxml reader

Fixed

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

[0.5.0] - 2023-09-20

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

[0.4.1] - 2023-07-06

Fixed

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

[0.4.0] - 2023-07-06

Added

• Add + operator support for PSMList
• Add utility functions for m/z-mass conversion in new module psm_utils.utils
• peptidoform: Catch ProFormaError and reraise PeptidoformException with invalid peptidoform in message

Changed

• io.msamanda: Changed REQUIRED_COLUMNS to include new features from the MS Amanda output CSV file
• io.peptide_recordCatch the IndexError when a modification has a position that is out of range for the peptide, and raise an InvalidPeprecModificationError instead.
• Rename optional dependency doc to docs
• Implement "raise from e" when applicable throughout package

Fixed

• Added missing io.msamanda API docs

[0.3.1] - 2023-06-19

Changed

• io.sage: Change spectrum_fdr to spectrum_q (crf. lazear/sage#64).

[0.3.0] - 2023-06-08

Added

• Add reader for Sage PSM files.
• io.mzid: Add reading/writing of PEP and q-values

Changed

• psm: The default values of PSM.provenance_data, PSM.metadata and PSM.rescoring_features are now dict() instead of None.
• PSMList: Also allow Numpy integers for indexing a single PSM
• io.mzid.MzidReader: Attempt to parse retention time or scan start time cvParams from both SpectrumIdentificationResult as SpectrumIdentificationItem levels. Note that according to the mzIdentML specification document (v1.1.1) neither cvParams are expected to be present at either level.
• io.mzid.MzidReader: Prefer spectrum title cvParam over spectrumID attribute for PSM.spectrum_id as these titles always match to the peak list files. In this case, spectrumID is saved in metadata["mzid_spectrum_id"]. Fall back to spectrumID if spectrum title is absent.
• io.mzid.MzidWriter: PSM.retention_time is now written as cvParam retention time instead of scan start time, and to the SpectrumIdentificationItem level instead of the SpectrumIdentificationResult level, as theoretically in psm_utils, multiple PSMs for the same spectrum can have different values for retention_time.
• io.mzid.MzidWriter: Write PSM score as cvParam search engine specific score instead of userParam score.
• io.percolator.PercolatorTabWriter: For PIN-style files: Use SpecId instead of PSMId and write PSMScore and ChargeN columns by default.
• Filter warnings from psims.mzmlb on import, as mzmlb is not used

Fixed

• psm: Fix missing qvalue and pep in docstring
• peptidoform: ProForma mass modifications are now correctly parsed within the rename_modifications function.
• io.maxquant.MSMSReader: Correctly parse empty Proteins column to None
• io.percolator.PercolatorTabReader: Correctly parse Percolator peptidoform notation if no leading or trailing amino acids are present (e.g. .ACDK. instead of K.ACDK.E).
• io.percolator.PercolatorTabWriter: ScanNr is now correctly written as an integer counting from the first PSM in the file.
• io.percolator.PercolatorTabWriter: If no protein information is present, write the peptidoform preceded by PEP_ to the Proteins column.
• io.idxml: Read metadata as strings
• io.mzid.MzidReader: Set PSM.retention_time to None instead of float('nan') if missing from the PSM file.
• io.mzid: Fix reading of file if charge is missing
• io.mzid: Fix writing if protein_list is None
• io.mzid: Consider all PeptideEvidence entries for a SpectrumIdentificationItem to determine is_decoy
• io.mzid: Fix handling of mzIdentML files when is_decoy field is not present (fixes #30)
• io.tsv: Raise PSMUtilsIOException with clear error message when TSV protein_list cannot be read

[0.2.3] - 2023-03-08

Fixed

• Fix bug in io._base_classes (introduced in v0.2.2)
• Fix bug in TSVReader for reading TSV files with empty protein_list

[0.2.2] - 2023-03-08

Fixed

• io.peptide_record: Fix bug where provenance item filename was not a string
• Various minor fixes after linting

[0.2.1] - 2023-01-17

Added

• Peptidoform: Add is_modified property

Fixed

• io.mzid: Fix issues when parsing Comet or MSAmanda-generated mzIdentML files and certain fields are missing.

[0.2.0] - 2022-11-12

Added

• PSM: Add ion_mobility field
• PSMList: Allow slicing with bool arrays (e.g., psm_df[psm_df["retention_time"] < 2000])
• rename_modifications: Add support for fixed modifications
• Add example files
• Online: Add support for GZipped files
• Online: Add support for logarithmic score (e.g. e-values)
• Docs: Extend contributing with example contributions
• Docs: Add notes to PSM.get_usi() method
• Docs: Extend quickstart on PSMList
• Docs: Add "psm_utils tags" for file formats, as used in high-level read/write/convert functions
• Docs: Peptide Record: add notes on unsupported modification types; add example for C-terminal modification
• Docs: More clearly document conversion to DataFrame
• Docs: Add bioconda install instructions
• Docs: Add citation for preprint
• Tests: Added tests for PSMList set_ranks and get_rank1_psms methods

Changed

• PSMList: Refactor set_ranks and get_rank1_psms methods
• Update .vscode/settings.json
• Typing: Replace Union with OR operator |
• Online: Use percentiles instead of randomly sampling for PP plot
• Docs: Force TOC-tree max depth
• Tests: Expand unit tests in general

Fixed

• PSMList: Truncate __repr__ to first five entries only, avoiding crashing notebook output
• Peptidoform: Minor typing fix
• add_fixed_modifications: Allow input as dict as well as list of tuples
• io: Fix issue where the NamedTemporaryFile for _supports_write_psm was seen as invalid Percolator file
• io.convert: pass progressbar argument to class, not write_file
• io.mzid: Add more supported MS-GF score names, make SpecEValue default
• io.peptide_record: spec_id is now a required column (spectrum_id is also required in PSM)
• io.peptide_record: Fix parsing of C-terminal modifications from proforma to peprec
• io.percolator: Fix Percolator peptide notation writing (fixes #18)
• io.tsv: Fix issue where TSVReader would not use string type for metadata
• io.xtandem: Fix issue where optional arguments were not accepted by XTandemReader
• io.xtandem: Do not split spectrum title on space
• io.xtandem: Fix issue where optional arguments were not accepted by XTandemReader
• Online: Fix pi-0 diagonal calculation
• Remove obsolete to do comments in code

[0.1.0] - 2022-10-14

Added

• Initial version