Psm-utils

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)

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

Fixed

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

Added

- `io`: Added new `io.pepxml` reader

Fixed

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

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

Fixed

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