v1.2.0

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)

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New Contributors

• @levitsky made their first contribution in #101
• @rodvrees made their first contribution in #103

Full Changelog: v1.1.1...v1.2.0

v1.1.1

Fixed

• io: Fix Sage filename pattern for automatic file type inference by @RalfG in #98
• io.flashlfq: Fix writing PSMs without protein accession by @RalfG in #98
• io.flashlfq: Fix column names Peptide Monoisotopic Mass and Protein Accession by @RalfG in #97
• io.idxml: Fix parsing if spectra file name not present by @jonasscheid in #99

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Full Changelog: v1.1.0...v1.1.1

v1.1.0

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.

v1.0.1

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).

v1.0.0

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

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

v0.9.1

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)

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New Contributors

• @julianu made their first contribution in #83

Full Changelog: v0.9.0...0.9.1

Important

This version was not correctly released to PyPI.

v0.9.0

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).

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Full Changelog: v0.8.3...v0.9.0

v0.8.3

Added

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

Changed

• Project infrastructure changes: Switch from Flit to Setuptools, use Ruff for linting on GitHub Actions, fix CodeCov.

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Full Changelog: v0.8.2...v0.8.3

v0.8.2

Added

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

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Full Changelog: v0.8.1...v0.8.2

v0.8.1

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)

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Full Changelog: v0.8.0...v0.8.1