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.
[0.4.0] - 2023-07-06
Added
Add + operator support for
PSMList
Add utility functions for m/z-mass conversion in new module
psm_utils.utils
peptidoform
: CatchProFormaError
and reraisePeptidoformException
with invalid peptidoform in message
Changed
io.msamanda
: ChangedREQUIRED_COLUMNS
to include new features from the MS Amanda output CSV fileio.peptide_record``Catch the ``IndexError
when a modification has a position that is out of range for the peptide, and raise anInvalidPeprecModificationError
instead.Rename optional dependency
doc
todocs
Implement “raise from e” when applicable throughout package
Fixed
Added missing
io.msamanda
API docs
[0.3.1] - 2023-06-19
Changed
io.sage
: Changespectrum_fdr
tospectrum_q
(crf. lazear/sage#64).
[0.3.0] - 2023-06-08
Added
Add reader for Sage PSM files.
io.mzid
: Add reading/writing of PEP and q-values
Changed
psm
: The default values ofPSM.provenance_data
,PSM.metadata
andPSM.rescoring_features
are nowdict()
instead ofNone
.PSMList
: Also allow Numpy integers for indexing a single PSMio.mzid.MzidReader
: Attempt to parseretention time
orscan 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
: Preferspectrum title
cvParam overspectrumID
attribute forPSM.spectrum_id
as these titles always match to the peak list files. In this case,spectrumID
is saved inmetadata["mzid_spectrum_id"]
. Fall back tospectrumID
ifspectrum title
is absent.io.mzid.MzidWriter
:PSM.retention_time
is now written as cvParamretention time
instead ofscan start time
, and to theSpectrumIdentificationItem
level instead of theSpectrumIdentificationResult
level, as theoretically in psm_utils, multiple PSMs for the same spectrum can have different values forretention_time
.io.mzid.MzidWriter
: Write PSM score as cvParamsearch engine specific score
instead of userParamscore
.io.percolator.PercolatorTabWriter: For PIN-style files: Use
SpecId
instead ofPSMId
and writePSMScore
andChargeN
columns by default.Filter warnings from
psims.mzmlb
on import, asmzmlb
is not used
Fixed
psm
: Fix missing qvalue and pep in docstringpeptidoform
: ProForma mass modifications are now correctly parsed within therename_modifications
function.io.maxquant.MSMSReader
: Correctly parse emptyProteins
column toNone
io.percolator.PercolatorTabReader
: Correctly parse Percolator peptidoform notation if no leading or trailing amino acids are present (e.g..ACDK.
instead ofK.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 byPEP_
to the Proteins column.io.idxml
: Read metadata as stringsio.mzid.MzidReader
: SetPSM.retention_time
toNone
instead offloat('nan')
if missing from the PSM file.io.mzid
: Fix reading of file if charge is missingio.mzid
: Fix writing if protein_list is Noneio.mzid
: Consider allPeptideEvidence
entries for aSpectrumIdentificationItem
to determineis_decoy
io.mzid
: Fix handling of mzIdentML files whenis_decoy
field is not present (fixes #30)io.tsv
: RaisePSMUtilsIOException
with clear error message when TSVprotein_list
cannot be read
[0.2.3] - 2023-03-08
Fixed
Fix bug in
io._base_classes
(introduced in v0.2.2)Fix bug in TSVReader for reading TSV files with empty protein_list
[0.2.2] - 2023-03-08
Fixed
io.peptide_record
: Fix bug where provenance itemfilename
was not a stringVarious minor fixes after linting
[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