v1.2.2

Update github release.yaml to fix bioconda

Full Changelog: v1.2.1...v1.2.2

Release v1.2.1

• set python version to python v3.11 in release.yml
• updates actions/checkout and actions/setup-python in release.yml

Release v1.2.0

Major changes

• Update of the supported python versions to python >=3.9 and <3.12
• The build system was changed to poetry (https://python-poetry.org/).
• NetMHCIIpan4.3 is now supported
• more granular calculation of mutated rna expression columns

Minor changes

• Patient file is now optional in epitope mode
• increase version of several python dependenices (biopython, pandas, numpy, scipy, pysam, cython)
• update of documentation
• improvement of warning and logging messages
• minor bug fixes

Release v1.1.0

Major changes

• Expression and VAF usage is now more clear and defined per output column
• External annotations are now kept in the epitope mode
• NeoFox now supports parsing of the newest versions of PRIME, MixMHCpred, MixMHC2pred
• MixMHC2pred is supported for mouse

Minor changes

• Update of column names in the output
• More columns of the netMHCpan / netMHCIIpan output are now provided in the NeoFox output (e.g. core)

Beta release v1.1.0b2

Changes:

• Extend support for more Python 3.8 bugfix versions

Beta release v1.1.0b1

Changes:

• Reimplement Hex in python to improve performance and robustness
• Fix several typos in the documentation
• Remove the undocumented field is_rna_available in the patient model
• Set more specific versions for some python dependencies

Release v1.0.2

Bugfixes

• set expression_mutated_transcript to use RNA VAF by default instead of DNA VAF. (Only versions v1.0.0 & v1.0.1 used DNA VAF by default. Versions < v.1.0.0 use RNA VAF by default)

v1.0.1

Bugfixes

• Fix the documentation. Now the documentation at readthedocs is up to date
• Fix crash in neoepitope mode when only either MHC-I or MHC-II epitopes were provided

Release v1.0.0

Major changes

• Added a model for epitopes
• Optionally, output a table with all annotated epitopes obtained from a set of input neoantigens (option --with-all-neoepitopes)
• Additional command line tool neofox-epitope that accepts epitopes as input. The epitopes may be associated with a particular HLA allele or alternatively paired with each of the HLA alleles defined in a given patient
• MHC-II weak binder threshold changed from 10 to 5
• Output JSON file with reference resources metadata with the aim of documenting the reference data versions

Minor changes

• Neoantigen model is simplified by removing the Mutation entity
• Annotations are renamed with the aim of making them more self explanatory
• Always output tabular and JSON data as opposed to choosing output format
• Input parameters --candidate-file and --json-file are simplified into --input-file. The format of the input is inferred from the file - extension, being valid extensions *.txt and *.tsv for tabular format; and *.json for JSON format.
• Recognition potential is now also annotated when mutation not in anchor positions
• Dask cluster is now closed in a cleaner way
• Some of the binaries are now optionally read from the PATH
• All temporary files from MHC prediction are removed now, this caused troubles for large datasets
• Now all relevant peptides of length 8-14 are considerd while MHC-I prediction (previously: 8-11)

Release v0.6.4

Changes

• Removes pickle-mixin from dependencies
• Upgrades pysam version to 0.19.1
• Fix biopython version to 0.19.1