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.

[0.4.1] - 2023-07-06

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

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

io.msamanda: Changed REQUIRED_COLUMNS to include new features from the MS Amanda output CSV file
io.peptide_record``Catch 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

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

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

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

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

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