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CHANGELOG
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v0.7.4
- Make --fasta_use_uniprot_id compatible with quantification
- Fix problem with missing delta mass column for andromeda2pin
- Add support for ms2rescore percolator format (#23)
- Refactored update_evidence_from_pout
- Remove unsupported mq_msms argument for update_evidence_from_pout
v0.7.3
- Fix nondeterministic behavior of decouple_connected_proteins
v0.7.2
- Add --protein_group_fdr_threshold flag to set the protein group-level FDR cutoff for the rescuing procedure and logging messages
- Fix compatibility with Oktoberfest's new ProForma N-terminal notation
- Improved ProForma sequence format support
- Support new oktoberfest psmid with optional scan event number
- Use --psm_fdr_cutoff for "Peptide counts (unique)" column
v0.7.1
- Switch to modified peptide instead of peptide in fragpipe parsing functions
- Make peptide flanking characters consistent across search engines. Fixes bug with percolator input used with --peptide_protein_map
v0.7.0
- Less strict llvmlite dependency
- Add functionality to requantify fragpipe combined_protein.tsv
- Fix random number seed for mokapot
- Major refactoring and linting of multiple scripts
- Add system tests
- Fix peptide_protein_map input option for quantification.py
- Refactor picked_group_fdr.py, add some unit tests
- Add --suppress_missing_peptide_warning to all relevant modules
- Add readthedocs documentation
- Allow combining multiple Sage or FragPipe searches
v0.6.6
- Revert return type to List for ProteinGroups.get_protein_groups
v0.6.5
- Fix check for peptides not assigned to any protein group
- Fix for docker interactive mode
v0.6.4
- Add filename column for andromeda2pin
- Update mokapot to 0.10.0
- Update packages in poetry.lock
- Fix docker package version in greeter
v0.6.3
- Skip lfq if only 1 experiment is present
- Fix organism fasta parsing
- Added fractionated sample support for sage
- Fix update_fragpipe_results
v0.6.2
- Update job-pool to v0.2.6 to fix hanging maxlfq quant
- Fix gene_level support in quantification.py
- Speed optimizations for digest.py
v0.6.1
- Fix `--gene-level` option
- Switch to job-pool package for multiprocessing
- Use specific libxml2 version to fix GUI build (#12)
v0.6.0
- Added support for FragPipe and Sage for LFQ data
- Support input files with byte order mark (#9)
- Added tool for entrapment FDR calculation and plotting
- Gui build fix (#8)
- Major code refactoring (camelCase to snake_case, new classes, better submodules)
v0.5.0
- Added support for proteases that cleave before an amino acid, e.g. Asp-N, Lys-N
- Fix for empty score field in evidence file
- Add better detection of maxquant evidence files (#7)
- Added support for combining evidence files with different proteases
- Updated GUI to support different digestion parameters per evidence file
- Fix log levels in GUI
- Added example scripts and notebook for book chapter analysis
- Add check for shared peptides to protein groups that were filtered out because they had no reliable peptides
- Change peptide count to use score cutoff for peptide FDR instead of protein FDR
- Improved log messages
v0.4.0
- Removed proteins without any PSMs below the FDR threshold from protein groups output. Setting the new `--keep_all_proteins` flag reverts to the old behavior.
- Added support for supplying multiple evidence files
- Added support for mokapot format and allow users to specify methods with custom toml files
- Add `--fasta_contains_decoys` flag and functionality
- Update llvmlite (#4)
v0.3.5
- Added rescoring input (e.g. Prosit results) to GUI
v0.3.4
- Added percolator input to GUI
v0.3.3
- Add option for multiple evidence files and selecting digestion parameters in GUI
v0.3.2
- Fix mokapot decoy filename
- Propagate argparse errors from pipeline scripts to logger
v0.3.1
- Fixed missing methods folder in GUI
v0.3.0
- Added make rules to reproduce manuscript figures
- Moved methods to toml files
- Update picking strategy to use leading proteins
- Add max_workers option for mokapot
- Add support for multiple threads in LFQ computation
- Fix non-functioning train_fdr option for mokapot
v0.2.7
- Added maxtasksperchild for better memory management in LFQ
v0.2.6
- Upgrade minimum Python version to 3.8 for new scipy version
- Reduced LFQ memory by 80% and speed up by 30%
v0.2.5
- Undo switching order of log and median operation in LFQ as this led to wrong results
v0.2.4
- Speed up LFQ by using Bottleneck package for nanmedian
v0.2.3
- Added unit and performance tests to repo
- Allow multithreading for LFQ quant
v0.2.2
- Upgrade minimum Python version to 3.7 to remove dataclasses dependency
v0.2.1
- Change requirements to inequalities for packages with 0.x version to allow better dependency resolving
v0.2.0
- Major improvements to GUI and removed unnecessary libraries to reduce file size
v0.1.0
- Initial release