issues
search
compomics
/
psm_utils
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
23
stars
6
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
`Peptidoform`: Add property/method to extract modified sequence without charge state
#93
RalfG
opened
4 days ago
0
NoneType object is not subcriptable
#92
prvst
opened
1 week ago
4
Update changelog
#91
RalfG
closed
1 week ago
0
Version bump
#90
RalfG
closed
1 week ago
1
Implement eq and getitem dunder methods for Peptidoform
#89
RalfG
closed
1 week ago
1
Improve TSV reading error handling
#88
RalfG
closed
1 week ago
1
comet support
#87
paretje
closed
1 month ago
1
fix warning when parsing tsv
#85
paretje
closed
1 month ago
0
Add indexing methods to psm_list object
#84
ArthurDeclercq
closed
2 weeks ago
1
pepXML or mzIdentML from Comet
#86
jke000
closed
1 month ago
3
fix parsing PSMs and complete protein names in XTandem
#83
julianu
closed
1 month ago
2
Remove temporary patch for caching Proforma modification resolvers
#82
RalfG
closed
3 months ago
1
Add Parquet reading and writing for efficient storage of PSM lists
#81
RalfG
closed
3 months ago
1
Update publish workflow to use build or setuptools instead of flit.
#80
RalfG
closed
4 months ago
0
Cache modification resolvers (temporary patch); version bump
#79
RalfG
closed
4 months ago
0
Project and CI changes
#78
RalfG
closed
4 months ago
1
Investigate parsing of mzIdentML `SubstituteModification` entries
#77
RalfG
opened
4 months ago
0
io.proteoscape: Parse filename into PSM run field
#76
RalfG
closed
4 months ago
0
ProteoScape / TIMScore improvements
#75
RalfG
closed
4 months ago
1
idXML updates
#74
RalfG
closed
4 months ago
0
Various bug fixes
#73
ArthurDeclercq
closed
5 months ago
1
Add support for globally-defined terminal modifications
#71
RalfG
closed
5 months ago
0
Add TIMScore Parquet support
#70
RalfG
closed
5 months ago
1
Fixes in `io.xtandem`
#69
RalfG
closed
5 months ago
0
Infer encoding of text-based files?
#68
RalfG
opened
6 months ago
0
Question: Best way to get seperate MSGF+ results (for target and decoy) to one psm_list
#67
JannikSchneider12
closed
5 months ago
1
`io.tsv`: Replace exception with logging
#66
ArthurDeclercq
closed
5 months ago
1
Question: How to deal with percolator output (xml)
#65
JannikSchneider12
closed
7 months ago
0
Getting Name Error with MSGFplus mzid file
#72
thulasis
closed
2 weeks ago
2
Add support for newer PD MSF file versions
#64
RalfG
opened
8 months ago
0
Fix bug in xtandem reader
#63
RalfG
closed
8 months ago
1
Fix xtandem `run` value parsing; fix renaming negative mass modifications
#62
ArthurDeclercq
closed
9 months ago
1
Convert numpy objects to float in idxml writer
#61
jonasscheid
closed
9 months ago
1
Updating metaValues of PeptideHits with numpy objects crashes in idxml writer
#60
jonasscheid
closed
9 months ago
0
Xtandem run fix
#59
ArthurDeclercq
closed
10 months ago
1
Add score_key argument to XTandemReader
#57
RalfG
closed
10 months ago
1
Fix reading of pepXML files without RT
#56
RalfG
closed
10 months ago
0
X!Tandem score is hyperscore instead of e-value
#55
tivdnbos
closed
10 months ago
1
Feature: Add PepXMLReader
#54
RalfG
closed
10 months ago
1
Pyteomics relies on Unimod web request
#53
jonasscheid
closed
10 months ago
1
Read and write idXML files using pyopenms
#52
jonasscheid
closed
10 months ago
3
version bump, changelog update
#51
ArthurDeclercq
closed
11 months ago
1
Fix warnings that arose during tests
#50
RalfG
closed
11 months ago
1
Add len and iter methods to Peptidoform; fix mzid score_key usage
#49
RalfG
closed
11 months ago
0
Improve TSV reader error handling
#48
RalfG
closed
11 months ago
0
Minor changes
#47
RalfG
closed
11 months ago
0
Update regex pattern in _parse_peptidoform in msamanda.py
#46
louisebuur
closed
11 months ago
1
Add support for terminal modifications in `Peptidoform.add_fixed_modifications`
#45
RalfG
opened
11 months ago
0
Add reader for Proteome Discoverer MSF files; other changes/fixes/additions
#44
RalfG
closed
11 months ago
0
Add ionbot reader; read ion mobility from mzid files
#43
ArthurDeclercq
closed
11 months ago
2
Next