Releases: compomics/psm_utils
Releases · compomics/psm_utils
v1.1.1
Fixed
io
: Fix Sage filename pattern for automatic file type inference by @RalfG in #98io.flashlfq
: Fix writing PSMs without protein accession by @RalfG in #98io.flashlfq
: Fix column namesPeptide Monoisotopic Mass
andProtein Accession
by @RalfG in #97io.idxml
: Fix parsing if spectra file name not present by @jonasscheid in #99
Full Changelog: v1.1.0...v1.1.1
v1.1.0
v1.0.1
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)
New Contributors
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 (newSageParquetReader
, renamedSageReader
toSageTSVReader
).
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).
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.
Full Changelog: v0.8.2...v0.8.3
v0.8.2
v0.8.1
Added
io.proteoscape
: AllowProteoScapeReader
instantiation from Pandas DataFrame and access PSM by index.
Fixed
- Remove accidental print statement.
io.idxml
: Fixed parenthesis in type hint
Changed
io.idxml
: FilterOPENMS_DATA_PATH
warnings (see compomics/ms2rescore#129 and OpenMS/OpenMS#7418)io.proteoscape
: Rename module fromTIMScore
toProteoScape
.io.proteoscape
: Use correct search engine score (x_corr_score
instead oftims_score
)
Full Changelog: v0.8.0...v0.8.1
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