Changelog¶
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.
[0.2.1] - 2023-01-17¶
Added¶
Peptidoform
: Addis_modified
property
Fixed¶
io.mzid
: Fix issues when parsing Comet or MSAmanda-generated mzIdentML files and certain fields are missing.
[0.2.0] - 2022-11-12¶
Added¶
PSM
: Addion_mobility
fieldPSMList
: Allow slicing with bool arrays (e.g.,psm_df[psm_df["retention_time"] < 2000]
)rename_modifications
: Add support for fixed modificationsAdd 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()
methodDocs: 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
andget_rank1_psms
methods
Changed¶
PSMList
: Refactorset_ranks
andget_rank1_psms
methodsUpdate
.vscode/settings.json
Typing: Replace Union with OR operator
|
Online: Use percentiles instead of randomly sampling for PP plot
Docs: Force TOC-tree max depth
Tests: Expand unit tests in general
Fixed¶
PSMList
: Truncate repr to first five entries only, avoiding crashing notebook outputPeptidoform
: Minor typing fixadd_fixed_modifications
: Allow input as dict as well as list of tuplesio
: Fix issue where theNamedTemporaryFile
for_supports_write_psm
was seen as invalid Percolator fileio.convert
: passprogressbar
argument to class, notwrite_file
io.mzid
: Add more supported MS-GF score names, make SpecEValue defaultio.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 peprecio.percolator
: Fix Percolator peptide notation writing (fixes #18)io.tsv
: Fix issue whereTSVReader
would not use string type for metadataio.xtandem
: Fix issue where optional arguments were not accepted byXTandemReader
io.xtandem
: Do not split spectrum title on spaceio.xtandem
: Fix issue where optional arguments were not accepted byXTandemReader
Online: Fix pi-0 diagonal calculation
Remove obsolete to do comments in code
[0.1.0] - 2022-10-14¶
Added¶
Initial version