diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml index 897c903..16407d0 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/pypi-publish.yml @@ -13,7 +13,7 @@ jobs: - name: Install utilities run: sudo apt-get install -y mmv - name: Set up Python 3.7 - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 with: python-version: 3.7 - name: Install pypa/build diff --git a/.github/workflows/python-test-conda-external.yml b/.github/workflows/python-test-conda-external.yml index 433833d..b057965 100644 --- a/.github/workflows/python-test-conda-external.yml +++ b/.github/workflows/python-test-conda-external.yml @@ -15,10 +15,10 @@ jobs: runs-on: ${{ matrix.platform }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: path: epytope - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 with: repository: kohlbacherlab/fred-tools token: ${{ secrets.FRED_CI_PAT }} diff --git a/.github/workflows/python-test-conda.yml b/.github/workflows/python-test-conda.yml index 7688447..6e06530 100644 --- a/.github/workflows/python-test-conda.yml +++ b/.github/workflows/python-test-conda.yml @@ -15,7 +15,7 @@ jobs: runs-on: ${{ matrix.platform }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set conda package directory run: | mkdir /tmp/condapkgs diff --git a/CHANGELOG.md b/CHANGELOG.md index 29cf4cc..3f6dda0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,19 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v3.4.0 - 2024-01-10 + +### `Added` + +- [#93](https://github.com/KohlbacherLab/epytope/pull/93) Added NetMHCIIpan version 4.2 interface [#92](https://github.com/KohlbacherLab/epytope/issues/92) +- [#96](https://github.com/KohlbacherLab/epytope/pull/96) Added NetMHCIIpan version 4.3 interface [#95](https://github.com/KohlbacherLab/epytope/issues/95) + +### `Changed` + +### `Fixed` + +- [#93](https://github.com/KohlbacherLab/epytope/pull/93) Fixed length restriction of NetMHCIIpan interfaces [#91](https://github.com/KohlbacherLab/epytope/issues/91) + ## v3.3.1 - 2023-04-25 ### `Added` diff --git a/README.md b/README.md index 8db4611..949e936 100644 --- a/README.md +++ b/README.md @@ -63,7 +63,7 @@ Currently **epytope** provides implementations of several prediction methods or - [NetMHC](https://pubmed.ncbi.nlm.nih.gov/26515819/) 3.0, 3.4, 4.0 - [NetMHCII](https://pubmed.ncbi.nlm.nih.gov/29315598/) 2.2, 2.3 - [NetMHCpan](https://pubmed.ncbi.nlm.nih.gov/28978689/) 2.4, 2.8, 3.0, 4.0, 4.1 - - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/32406916/) 3.0, 3.1, 4.0, 4.1 + - [NetMHCIIpan](https://pubmed.ncbi.nlm.nih.gov/38000035/) 3.0, 3.1, 4.0, 4.1, 4.2, 4.3 - [PickPocket](https://pubmed.ncbi.nlm.nih.gov/19297351/) 1.1 - [NetCTLpan](https://pubmed.ncbi.nlm.nih.gov/20379710/) 1.1 - Epitope Selection diff --git a/epytope/Data/supportedAlleles/external/netmhcIIpan_4_2.py b/epytope/Data/supportedAlleles/external/netmhcIIpan_4_2.py new file mode 100644 index 0000000..4b0c2d5 --- /dev/null +++ b/epytope/Data/supportedAlleles/external/netmhcIIpan_4_2.py @@ -0,0 +1,2 @@ +netmhcIIpan_4_2 = frozenset(['HLA-DPA1*01:03-DPB1*01:01', 'HLA-DPA1*01:03-DPB1*02:01', 'HLA-DPA1*01:03-DPB1*02:02', 'HLA-DPA1*01:03-DPB1*03:01', 'HLA-DPA1*01:03-DPB1*04:01', 'HLA-DPA1*01:03-DPB1*04:02', 'HLA-DPA1*01:03-DPB1*05:01', 'HLA-DPA1*01:03-DPB1*06:01', 'HLA-DPA1*01:03-DPB1*08:01', 'HLA-DPA1*01:03-DPB1*09:01', 'HLA-DPA1*01:03-DPB1*10:00', 'HLA-DPA1*01:03-DPB1*10:01', 'HLA-DPA1*01:03-DPB1*10:10', 'HLA-DPA1*01:03-DPB1*10:20', 'HLA-DPA1*01:03-DPB1*10:30', 'HLA-DPA1*01:03-DPB1*10:40', 'HLA-DPA1*01:03-DPB1*10:50', 'HLA-DPA1*01:03-DPB1*10:60', 'HLA-DPA1*01:03-DPB1*10:70', 'HLA-DPA1*01:03-DPB1*10:80', 'HLA-DPA1*01:03-DPB1*10:90', 'HLA-DPA1*01:03-DPB1*11:00', 'HLA-DPA1*01:03-DPB1*11:01', 'HLA-DPA1*01:03-DPB1*11:10', 'HLA-DPA1*01:03-DPB1*11:20', 'HLA-DPA1*01:03-DPB1*11:30', 'HLA-DPA1*01:03-DPB1*11:40', 'HLA-DPA1*01:03-DPB1*11:50', 'HLA-DPA1*01:03-DPB1*11:60', 'HLA-DPA1*01:03-DPB1*11:70', 'HLA-DPA1*01:03-DPB1*11:80', 'HLA-DPA1*01:03-DPB1*11:90', 'HLA-DPA1*01:03-DPB1*12:10', 'HLA-DPA1*01:03-DPB1*12:20', 'HLA-DPA1*01:03-DPB1*12:30', 'HLA-DPA1*01:03-DPB1*12:40', 'HLA-DPA1*01:03-DPB1*12:50', 'HLA-DPA1*01:03-DPB1*12:60', 'HLA-DPA1*01:03-DPB1*12:70', 'HLA-DPA1*01:03-DPB1*12:80', 'HLA-DPA1*01:03-DPB1*12:90', 'HLA-DPA1*01:03-DPB1*13:00', 'HLA-DPA1*01:03-DPB1*13:01', 'HLA-DPA1*01:03-DPB1*13:10', 'HLA-DPA1*01:03-DPB1*13:20', 'HLA-DPA1*01:03-DPB1*13:30', 'HLA-DPA1*01:03-DPB1*13:40', 'HLA-DPA1*01:03-DPB1*14:01', 'HLA-DPA1*01:03-DPB1*15:01', 'HLA-DPA1*01:03-DPB1*16:01', 'HLA-DPA1*01:03-DPB1*17:01', 'HLA-DPA1*01:03-DPB1*18:01', 'HLA-DPA1*01:03-DPB1*19:01', 'HLA-DPA1*01:03-DPB1*20:01', 'HLA-DPA1*01:03-DPB1*21:01', 'HLA-DPA1*01:03-DPB1*22:01', 'HLA-DPA1*01:03-DPB1*23:01', 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'HLA-DRB1*04:90', 'HLA-DRB1*04:91', 'HLA-DRB1*04:92', 'HLA-DRB1*04:93', 'HLA-DRB1*04:95', 'HLA-DRB1*04:96', 'HLA-DRB1*04:97', 'HLA-DRB1*04:98', 'HLA-DRB1*04:99', 'HLA-DRB1*07:01', 'HLA-DRB1*07:03', 'HLA-DRB1*07:04', 'HLA-DRB1*07:05', 'HLA-DRB1*07:06', 'HLA-DRB1*07:07', 'HLA-DRB1*07:08', 'HLA-DRB1*07:09', 'HLA-DRB1*07:10', 'HLA-DRB1*07:11', 'HLA-DRB1*07:12', 'HLA-DRB1*07:13', 'HLA-DRB1*07:14', 'HLA-DRB1*07:15', 'HLA-DRB1*07:16', 'HLA-DRB1*07:17', 'HLA-DRB1*07:18', 'HLA-DRB1*07:19', 'HLA-DRB1*07:20', 'HLA-DRB1*07:21', 'HLA-DRB1*07:22', 'HLA-DRB1*07:23', 'HLA-DRB1*07:24', 'HLA-DRB1*07:25', 'HLA-DRB1*07:27', 'HLA-DRB1*07:28', 'HLA-DRB1*07:29', 'HLA-DRB1*07:30', 'HLA-DRB1*07:31', 'HLA-DRB1*07:32', 'HLA-DRB1*07:33', 'HLA-DRB1*07:34', 'HLA-DRB1*07:35', 'HLA-DRB1*07:36', 'HLA-DRB1*07:37', 'HLA-DRB1*07:38', 'HLA-DRB1*07:39', 'HLA-DRB1*07:40', 'HLA-DRB1*07:41', 'HLA-DRB1*07:42', 'HLA-DRB1*07:43', 'HLA-DRB1*07:44', 'HLA-DRB1*07:45', 'HLA-DRB1*07:46', 'HLA-DRB1*07:47', 'HLA-DRB1*07:48', 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'HLA-DRB1*11:38', 'HLA-DRB1*11:39', 'HLA-DRB1*11:41', 'HLA-DRB1*11:42', 'HLA-DRB1*11:43', 'HLA-DRB1*11:44', 'HLA-DRB1*11:45', 'HLA-DRB1*11:46', 'HLA-DRB1*11:47', 'HLA-DRB1*11:48', 'HLA-DRB1*11:49', 'HLA-DRB1*11:50', 'HLA-DRB1*11:51', 'HLA-DRB1*11:52', 'HLA-DRB1*11:53', 'HLA-DRB1*11:54', 'HLA-DRB1*11:55', 'HLA-DRB1*11:56', 'HLA-DRB1*11:57', 'HLA-DRB1*11:58', 'HLA-DRB1*11:59', 'HLA-DRB1*11:60', 'HLA-DRB1*11:61', 'HLA-DRB1*11:62', 'HLA-DRB1*11:63', 'HLA-DRB1*11:64', 'HLA-DRB1*11:65', 'HLA-DRB1*11:66', 'HLA-DRB1*11:67', 'HLA-DRB1*11:68', 'HLA-DRB1*11:69', 'HLA-DRB1*11:70', 'HLA-DRB1*11:72', 'HLA-DRB1*11:73', 'HLA-DRB1*11:74', 'HLA-DRB1*11:75', 'HLA-DRB1*11:76', 'HLA-DRB1*11:77', 'HLA-DRB1*11:78', 'HLA-DRB1*11:79', 'HLA-DRB1*11:80', 'HLA-DRB1*11:81', 'HLA-DRB1*11:82', 'HLA-DRB1*11:83', 'HLA-DRB1*11:84', 'HLA-DRB1*11:85', 'HLA-DRB1*11:86', 'HLA-DRB1*11:87', 'HLA-DRB1*11:88', 'HLA-DRB1*11:89', 'HLA-DRB1*11:90', 'HLA-DRB1*11:91', 'HLA-DRB1*11:92', 'HLA-DRB1*11:93', 'HLA-DRB1*11:94', 'HLA-DRB1*11:95', 'HLA-DRB1*11:96', 'HLA-DRB1*11:97', 'HLA-DRB1*11:98', 'HLA-DRB1*11:99', 'HLA-DRB1*12:01', 'HLA-DRB1*12:02', 'HLA-DRB1*12:03', 'HLA-DRB1*12:04', 'HLA-DRB1*12:05', 'HLA-DRB1*12:06', 'HLA-DRB1*12:07', 'HLA-DRB1*12:08', 'HLA-DRB1*12:09', 'HLA-DRB1*12:10', 'HLA-DRB1*12:11', 'HLA-DRB1*12:12', 'HLA-DRB1*12:13', 'HLA-DRB1*12:14', 'HLA-DRB1*12:15', 'HLA-DRB1*12:16', 'HLA-DRB1*12:17', 'HLA-DRB1*12:18', 'HLA-DRB1*12:19', 'HLA-DRB1*12:20', 'HLA-DRB1*12:21', 'HLA-DRB1*12:22', 'HLA-DRB1*12:23', 'HLA-DRB1*12:25', 'HLA-DRB1*12:26', 'HLA-DRB1*12:27', 'HLA-DRB1*12:28', 'HLA-DRB1*12:29', 'HLA-DRB1*12:30', 'HLA-DRB1*12:32', 'HLA-DRB1*12:33', 'HLA-DRB1*12:34', 'HLA-DRB1*12:35', 'HLA-DRB1*12:36', 'HLA-DRB1*12:37', 'HLA-DRB1*12:38', 'HLA-DRB1*12:39', 'HLA-DRB1*12:40', 'HLA-DRB1*12:41', 'HLA-DRB1*12:42', 'HLA-DRB1*12:43', 'HLA-DRB1*12:44', 'HLA-DRB1*12:45', 'HLA-DRB1*12:46', 'HLA-DRB1*12:47', 'HLA-DRB1*12:48', 'HLA-DRB1*12:49', 'HLA-DRB1*12:50', 'HLA-DRB1*12:51', 'HLA-DRB1*12:52', 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'HLA-DRB1*13:15', 'HLA-DRB1*13:16', 'HLA-DRB1*13:17', 'HLA-DRB1*13:18', 'HLA-DRB1*13:19', 'HLA-DRB1*13:20', 'HLA-DRB1*13:21', 'HLA-DRB1*13:22', 'HLA-DRB1*13:23', 'HLA-DRB1*13:24', 'HLA-DRB1*13:25', 'HLA-DRB1*13:26', 'HLA-DRB1*13:27', 'HLA-DRB1*13:28', 'HLA-DRB1*13:29', 'HLA-DRB1*13:30', 'HLA-DRB1*13:31', 'HLA-DRB1*13:32', 'HLA-DRB1*13:33', 'HLA-DRB1*13:34', 'HLA-DRB1*13:35', 'HLA-DRB1*13:36', 'HLA-DRB1*13:37', 'HLA-DRB1*13:38', 'HLA-DRB1*13:39', 'HLA-DRB1*13:40', 'HLA-DRB1*13:41', 'HLA-DRB1*13:42', 'HLA-DRB1*13:43', 'HLA-DRB1*13:44', 'HLA-DRB1*13:45', 'HLA-DRB1*13:46', 'HLA-DRB1*13:47', 'HLA-DRB1*13:48', 'HLA-DRB1*13:49', 'HLA-DRB1*13:50', 'HLA-DRB1*13:51', 'HLA-DRB1*13:52', 'HLA-DRB1*13:53', 'HLA-DRB1*13:54', 'HLA-DRB1*13:55', 'HLA-DRB1*13:56', 'HLA-DRB1*13:57', 'HLA-DRB1*13:58', 'HLA-DRB1*13:59', 'HLA-DRB1*13:60', 'HLA-DRB1*13:61', 'HLA-DRB1*13:62', 'HLA-DRB1*13:63', 'HLA-DRB1*13:64', 'HLA-DRB1*13:65', 'HLA-DRB1*13:66', 'HLA-DRB1*13:67', 'HLA-DRB1*13:68', 'HLA-DRB1*13:69', 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'HLA-DRB3*02:14', 'HLA-DRB3*02:15', 'HLA-DRB3*02:16', 'HLA-DRB3*02:17', 'HLA-DRB3*02:18', 'HLA-DRB3*02:19', 'HLA-DRB3*02:20', 'HLA-DRB3*02:21', 'HLA-DRB3*02:22', 'HLA-DRB3*02:23', 'HLA-DRB3*02:24', 'HLA-DRB3*02:25', 'HLA-DRB3*02:26', 'HLA-DRB3*02:27', 'HLA-DRB3*02:28', 'HLA-DRB3*02:30', 'HLA-DRB3*02:31', 'HLA-DRB3*02:32', 'HLA-DRB3*02:33', 'HLA-DRB3*02:34', 'HLA-DRB3*02:35', 'HLA-DRB3*02:36', 'HLA-DRB3*02:37', 'HLA-DRB3*02:38', 'HLA-DRB3*02:39', 'HLA-DRB3*02:40', 'HLA-DRB3*02:41', 'HLA-DRB3*02:42', 'HLA-DRB3*02:43', 'HLA-DRB3*02:44', 'HLA-DRB3*02:45', 'HLA-DRB3*02:46', 'HLA-DRB3*02:47', 'HLA-DRB3*02:48', 'HLA-DRB3*02:49', 'HLA-DRB3*02:50', 'HLA-DRB3*02:51', 'HLA-DRB3*02:52', 'HLA-DRB3*02:53', 'HLA-DRB3*02:54', 'HLA-DRB3*02:56', 'HLA-DRB3*02:57', 'HLA-DRB3*02:58', 'HLA-DRB3*02:59', 'HLA-DRB3*02:60', 'HLA-DRB3*02:61', 'HLA-DRB3*02:62', 'HLA-DRB3*02:63', 'HLA-DRB3*02:64', 'HLA-DRB3*02:65', 'HLA-DRB3*02:66', 'HLA-DRB3*02:68', 'HLA-DRB3*02:69', 'HLA-DRB3*02:70', 'HLA-DRB3*02:71', 'HLA-DRB3*02:72', 'HLA-DRB3*02:73', 'HLA-DRB3*02:74', 'HLA-DRB3*02:75', 'HLA-DRB3*02:76', 'HLA-DRB3*02:77', 'HLA-DRB3*02:78', 'HLA-DRB3*02:79', 'HLA-DRB3*02:81', 'HLA-DRB3*02:82', 'HLA-DRB3*02:83', 'HLA-DRB3*02:84', 'HLA-DRB3*02:85', 'HLA-DRB3*02:86', 'HLA-DRB3*02:87', 'HLA-DRB3*02:88', 'HLA-DRB3*02:89', 'HLA-DRB3*02:90', 'HLA-DRB3*02:91', 'HLA-DRB3*02:92', 'HLA-DRB3*02:93', 'HLA-DRB3*02:94', 'HLA-DRB3*02:96', 'HLA-DRB3*02:97', 'HLA-DRB3*02:98', 'HLA-DRB3*02:99', 'HLA-DRB3*03:01', 'HLA-DRB3*03:03', 'HLA-DRB3*03:04', 'HLA-DRB3*03:05', 'HLA-DRB3*03:06', 'HLA-DRB3*03:07', 'HLA-DRB3*03:08', 'HLA-DRB3*03:09', 'HLA-DRB3*03:10', 'HLA-DRB3*03:11', 'HLA-DRB3*03:12', 'HLA-DRB3*03:13', 'HLA-DRB3*03:14', 'HLA-DRB3*03:15', 'HLA-DRB3*03:16', 'HLA-DRB3*03:17', 'HLA-DRB3*03:18', 'HLA-DRB3*03:19', 'HLA-DRB3*03:20', 'HLA-DRB3*03:21', 'HLA-DRB3*03:23', 'HLA-DRB3*03:24', 'HLA-DRB3*03:25', 'HLA-DRB3*03:26', 'HLA-DRB3*03:27', 'HLA-DRB3*03:28', 'HLA-DRB3*03:29', 'HLA-DRB3*03:31', 'HLA-DRB3*03:32', 'HLA-DRB3*03:33', 'HLA-DRB3*03:34', 'HLA-DRB3*03:35', 'HLA-DRB3*03:36', 'HLA-DRB3*03:37', 'HLA-DRB3*03:38', 'HLA-DRB3*03:39', 'HLA-DRB3*03:40', 'HLA-DRB3*03:41', 'HLA-DRB3*03:42', 'HLA-DRB3*03:43', 'HLA-DRB3*03:44', 'HLA-DRB3*03:45', 'HLA-DRB3*03:46', 'HLA-DRB3*03:47', 'HLA-DRB3*03:48', 'HLA-DRB3*03:49', 'HLA-DRB3*03:50', 'HLA-DRB3*03:51', 'HLA-DRB3*03:52', 'HLA-DRB3*03:53', 'HLA-DRB3*03:54', 'HLA-DRB3*03:55', 'HLA-DRB4*01:01', 'HLA-DRB4*01:02', 'HLA-DRB4*01:03', 'HLA-DRB4*01:04', 'HLA-DRB4*01:06', 'HLA-DRB4*01:07', 'HLA-DRB4*01:08', 'HLA-DRB4*01:09', 'HLA-DRB4*01:10', 'HLA-DRB4*01:11', 'HLA-DRB4*01:12', 'HLA-DRB4*01:13', 'HLA-DRB4*01:14', 'HLA-DRB4*01:15', 'HLA-DRB4*01:17', 'HLA-DRB4*01:18', 'HLA-DRB4*01:19', 'HLA-DRB4*01:20', 'HLA-DRB4*01:21', 'HLA-DRB4*01:22', 'HLA-DRB4*01:23', 'HLA-DRB4*01:24', 'HLA-DRB4*01:25', 'HLA-DRB4*01:26', 'HLA-DRB4*01:27', 'HLA-DRB4*01:28', 'HLA-DRB4*01:29', 'HLA-DRB4*01:30', 'HLA-DRB4*01:31', 'HLA-DRB4*01:32', 'HLA-DRB4*01:33', 'HLA-DRB4*01:34', 'HLA-DRB4*01:35', 'HLA-DRB4*01:36', 'HLA-DRB4*01:37', 'HLA-DRB4*01:39', 'HLA-DRB4*01:40', 'HLA-DRB4*01:41', 'HLA-DRB4*01:42', 'HLA-DRB4*01:43', 'HLA-DRB4*01:44', 'HLA-DRB4*01:45', 'HLA-DRB4*01:46', 'HLA-DRB4*01:47', 'HLA-DRB4*01:48', 'HLA-DRB4*01:49', 'HLA-DRB4*01:50', 'HLA-DRB4*01:51', 'HLA-DRB4*01:52', 'HLA-DRB4*01:53', 'HLA-DRB4*01:54', 'HLA-DRB4*01:55', 'HLA-DRB4*01:58', 'HLA-DRB4*01:59', 'HLA-DRB4*01:60', 'HLA-DRB4*01:62', 'HLA-DRB4*01:63', 'HLA-DRB4*01:64', 'HLA-DRB4*01:66', 'HLA-DRB4*01:67', 'HLA-DRB4*01:68', 'HLA-DRB4*01:69', 'HLA-DRB4*01:70', 'HLA-DRB4*01:72', 'HLA-DRB4*01:73', 'HLA-DRB4*01:74', 'HLA-DRB4*01:75', 'HLA-DRB4*01:76', 'HLA-DRB4*01:77', 'HLA-DRB4*01:78', 'HLA-DRB4*01:79', 'HLA-DRB4*01:81', 'HLA-DRB4*01:82', 'HLA-DRB4*01:83', 'HLA-DRB4*01:85', 'HLA-DRB4*01:86', 'HLA-DRB4*01:87', 'HLA-DRB4*01:88', 'HLA-DRB4*01:89', 'HLA-DRB4*01:90', 'HLA-DRB4*01:91', 'HLA-DRB4*01:92', 'HLA-DRB4*01:93', 'HLA-DRB4*01:94', 'HLA-DRB4*01:95', 'HLA-DRB4*01:96', 'HLA-DRB4*01:97', 'HLA-DRB4*01:98', 'HLA-DRB4*01:99', 'HLA-DRB5*01:01', 'HLA-DRB5*01:02', 'HLA-DRB5*01:03', 'HLA-DRB5*01:04', 'HLA-DRB5*01:05', 'HLA-DRB5*01:06', 'HLA-DRB5*01:08', 'HLA-DRB5*01:10', 'HLA-DRB5*01:11', 'HLA-DRB5*01:12', 'HLA-DRB5*01:13', 'HLA-DRB5*01:14', 'HLA-DRB5*01:15', 'HLA-DRB5*01:16', 'HLA-DRB5*01:17', 'HLA-DRB5*01:18', 'HLA-DRB5*01:19', 'HLA-DRB5*01:20', 'HLA-DRB5*01:21', 'HLA-DRB5*01:22', 'HLA-DRB5*01:23', 'HLA-DRB5*01:24', 'HLA-DRB5*01:25', 'HLA-DRB5*01:26', 'HLA-DRB5*01:28', 'HLA-DRB5*01:29', 'HLA-DRB5*01:30', 'HLA-DRB5*01:31', 'HLA-DRB5*01:32', 'HLA-DRB5*01:33', 'HLA-DRB5*01:34', 'HLA-DRB5*01:35', 'HLA-DRB5*01:36', 'HLA-DRB5*01:37', 'HLA-DRB5*01:38', 'HLA-DRB5*01:39', 'HLA-DRB5*01:40', 'HLA-DRB5*01:41', 'HLA-DRB5*01:42', 'HLA-DRB5*01:43', 'HLA-DRB5*01:44', 'HLA-DRB5*01:45', 'HLA-DRB5*01:46', 'HLA-DRB5*01:47', 'HLA-DRB5*01:50', 'HLA-DRB5*01:51', 'HLA-DRB5*01:54', 'HLA-DRB5*01:55', 'HLA-DRB5*01:56', 'HLA-DRB5*01:57', 'HLA-DRB5*01:59', 'HLA-DRB5*01:60', 'HLA-DRB5*01:61', 'HLA-DRB5*01:62', 'HLA-DRB5*01:63', 'HLA-DRB5*01:64', 'HLA-DRB5*01:65', 'HLA-DRB5*01:66', 'HLA-DRB5*01:69', 'HLA-DRB5*01:70', 'HLA-DRB5*01:72', 'HLA-DRB5*01:73', 'HLA-DRB5*01:74', 'HLA-DRB5*01:75', 'HLA-DRB5*01:76', 'HLA-DRB5*01:77', 'HLA-DRB5*01:78', 'HLA-DRB5*01:80', 'HLA-DRB5*01:82', 'HLA-DRB5*01:84', 'HLA-DRB5*01:85', 'HLA-DRB5*01:86', 'HLA-DRB5*01:87', 'HLA-DRB5*01:88', 'HLA-DRB5*01:89', 'HLA-DRB5*01:90', 'HLA-DRB5*01:91', 'HLA-DRB5*01:93', 'HLA-DRB5*01:94', 'HLA-DRB5*01:95', 'HLA-DRB5*01:96', 'HLA-DRB5*01:97', 'HLA-DRB5*01:98', 'HLA-DRB5*01:99', 'HLA-DRB5*02:02', 'HLA-DRB5*02:03', 'HLA-DRB5*02:04', 'HLA-DRB5*02:05', 'HLA-DRB5*02:06', 'HLA-DRB5*02:07', 'HLA-DRB5*02:08', 'HLA-DRB5*02:09', 'HLA-DRB5*02:10', 'HLA-DRB5*02:11', 'HLA-DRB5*02:12', 'HLA-DRB5*02:13', 'HLA-DRB5*02:14', 'HLA-DRB5*02:15', 'HLA-DRB5*02:16', 'HLA-DRB5*02:17', 'HLA-DRB5*02:18', 'HLA-DRB5*02:20', 'HLA-DRB5*02:21', 'HLA-DRB5*02:22', 'HLA-DRB5*02:23', 'HLA-DRB5*02:24', 'HLA-DRB5*02:27', 'HLA-DRB5*02:28', 'HLA-DRB5*02:29', 'HLA-DRB5*02:30', 'HLA-DRB5*02:31', 'H-2-IAb', 'H-2-IAd', +'H-2-IAk', 'H-2-IAq', 'H-2-IAs', 'H-2-IAu', 'H-2-IEd', 'H-2-IEk']) \ No newline at end of file diff --git a/epytope/EpitopePrediction/External.py b/epytope/EpitopePrediction/External.py index 344c3e1..d286dc6 100755 --- a/epytope/EpitopePrediction/External.py +++ b/epytope/EpitopePrediction/External.py @@ -1493,7 +1493,7 @@ class NetMHCIIpan_4_0(NetMHCIIpan_3_1): """ __name = "netmhcIIpan" __version = "4.0" - __supported_length = frozenset([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) + __supported_length = frozenset(list(range(9,57))) __allele_import_name = f"{__name}_{__version}".replace('.', '_') __alleles = getattr(__import__("epytope.Data.supportedAlleles.external." + __allele_import_name, fromlist=[__allele_import_name]) @@ -1597,6 +1597,81 @@ def parse_external_result(self, file): return result +class NetMHCIIpan_4_2(NetMHCIIpan_4_1): + """ + Implementation of NetMHCIIpan 4.2 adapter. + """ + __name = "netmhcIIpan" + __version = "4.2" + __supported_length = frozenset(list(range(9,57))) + __allele_import_name = f"{__name}_{__version}".replace('.', '_') + __alleles = getattr(__import__("epytope.Data.supportedAlleles.external." + __allele_import_name, + fromlist=[__allele_import_name]) + , __allele_import_name) + + __command = "netMHCIIpan -f {peptides} -inptype 1 -a {alleles} {options} -xls -xlsfile {out}" + + + @property + def version(self): + """The version of the predictor""" + return self.__version + + @property + def command(self): + """ + Defines the commandline call for external tool + """ + return self.__command + + +class NetMHCIIpan_4_3(NetMHCIIpan_4_2): + """ + Implementation of NetMHCIIpan 4.3 adapter. + """ + __name = "netmhcIIpan" + __version = "4.3" + __supported_length = frozenset(list(range(9,57))) + + __command = "netMHCIIpan -f {peptides} -inptype 1 -a {alleles} {options} -xls -xlsfile {out}" + + @property + def version(self): + """The version of the predictor""" + return self.__version + + @property + def command(self): + """ + Defines the commandline call for external tool + """ + return self.__command + + def parse_external_result(self, file): + """ + Parses external results and returns the result containing the predictors string representation + of alleles and peptides. + + :param str file: The file path or the external prediction results + :return: A dictionary containing the prediction results + :rtype: dict + """ + f = csv.reader(open(file, "r"), delimiter='\t') + scores = defaultdict(defaultdict) + ranks = defaultdict(defaultdict) + alleles = [x for x in set([x for x in next(f) if x != ""])] + next(f) + for row in f: + pep_seq = row[PeptideIndex.NETMHCIIPAN_4_3] + for i, a in enumerate(alleles): + scores[a][pep_seq] = float(row[ScoreIndex.NETMHCIIPAN_4_3 + i * Offset.NETMHCIIPAN_4_3]) + ranks[a][pep_seq] = float(row[RankIndex.NETMHCIIPAN_4_3 + i * Offset.NETMHCIIPAN_4_3]) + # Create dictionary with hierarchy: {'Allele1': {'Score': {'Pep1': Score1, 'Pep2': Score2,..}, 'Rank': {'Pep1': RankScore1, 'Pep2': RankScore2,..}}, 'Allele2':...} + result = {allele: {metric:(list(scores.values())[j] if metric == "Score" else list(ranks.values())[j]) for metric in ["Score", "Rank"]} for j, allele in enumerate(alleles)} + + return result + + class PickPocket_1_1(AExternalEpitopePrediction): """ Implementation of PickPocket adapter. @@ -1886,6 +1961,7 @@ class PeptideIndex(IntEnum): NETMHCIIPAN_3_1 = 1 NETMHCIIPAN_4_0 = 1 NETMHCIIPAN_4_1 = 1 + NETMHCIIPAN_4_3 = 1 PICKPOCKET_1_1 = 2 NETCTLPAN_1_1 = 3 @@ -1907,6 +1983,7 @@ class ScoreIndex(IntEnum): NETMHCIIPAN_3_1 = 3 NETMHCIIPAN_4_0 = 4 NETMHCIIPAN_4_1 = 5 + NETMHCIIPAN_4_3 = 6 PICKPOCKET_1_1 = 4 NETCTLPAN_1_1 = 7 @@ -1924,6 +2001,7 @@ class RankIndex(IntEnum): NETMHCIIPAN_3_1 = 5 NETMHCIIPAN_4_0 = 5 NETMHCIIPAN_4_1 = 6 + NETMHCIIPAN_4_3 = 7 class Offset(IntEnum): """ @@ -1941,6 +2019,7 @@ class Offset(IntEnum): NETMHCIIPAN_3_1 = 3 NETMHCIIPAN_4_0 = 2 NETMHCIIPAN_4_1 = 3 + NETMHCIIPAN_4_3 = 3 class HLAIndex(IntEnum): """ diff --git a/epytope/test/TestSpacerDesign.py b/epytope/test/TestSpacerDesign.py index 6755537..c558bfd 100644 --- a/epytope/test/TestSpacerDesign.py +++ b/epytope/test/TestSpacerDesign.py @@ -33,7 +33,10 @@ def test_standart_functions(self): sbws = EpitopeAssemblyWithSpacer(self.epis, cl_pred, epi_pred, self.alleles, solver="glpk") sol = sbws.solve() print(sol) - assert all(i == str(j) for i, j in zip(["GHRMAWDM", "WWQW", "VYEADDVI"], sol)) + test1 = all(i == str(j) for i, j in zip(["GHRMAWDM", "WWQW", "VYEADDVI"], sol)) + test2 = all(i == str(j) for i, j in zip(["GHRMAWDM", "WWRW", "VYEADDVI"], sol)) + + assert (test1 or test2) def test_unsupported_allele_length_combination(self): """ diff --git a/epytope/tutorials/EpitopePrediction.ipynb b/epytope/tutorials/EpitopePrediction.ipynb index fb174c8..cb80e91 100644 --- a/epytope/tutorials/EpitopePrediction.ipynb +++ b/epytope/tutorials/EpitopePrediction.ipynb @@ -202,10 +202,10 @@ "output_type": "stream", "text": [ "netmhc 3.0a,3.4,4.0\n", - "netmhcpan 2.4,2.8,3.0,4.0\n", + "netmhcpan 2.4,2.8,3.0,4.0,4.1\n", "netmhcstabpan 1.0\n", "netmhcii 2.2\n", - "netmhciipan 3.0,3.1\n", + "netmhciipan 3.0,3.1,4.0,4.1,4.2,4.3\n", "pickpocket 1.1\n", "netctlpan 1.1\n", "syfpeithi 1.0\n", @@ -1085,7 +1085,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.13" + "version": "3.7.12" } }, "nbformat": 4, diff --git a/setup.py b/setup.py index c432465..1e71d0d 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ name='epytope', # Version: - version='3.3.1', + version='3.4.0', description='A Framework for Epitope Detection and Vaccine Design', long_description=long_description, @@ -32,11 +32,11 @@ # Author details author='Benjamin Schubert, Mathias Walzer, Christopher Mohr, Leon Kuchenbecker', - author_email='benjamin.schubert@helmholtz-muenchen.de, walzer@ebi.ac.uk, christopher.mohr@uni-tuebingen.de, leon.kuchenbecker@uni-tuebingen.de ', + author_email='benjamin.schubert@helmholtz-muenchen.de, walzer@ebi.ac.uk, contact.cmohr@gmail.com, leon.kuchenbecker@uni-tuebingen.de ', # maintainer details - maintainer='Christopher Mohr', - maintainer_email='christopher.mohr@uni-tuebingen.de', + maintainer='Christopher Mohr, Jonas Scheid', + maintainer_email='contact.cmohr@gmail.com, jonas.scheid@uni-tuebingen.de', # Choose your license license='BSD',