- `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
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
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
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
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
Added
- Speed up mass calculation for large datasets by caching Proforma modification resolvers. Temporary patch until implemented in Pyteomics (see levitsky/pyteomics147).