Merge pull request #98 from KohlbacherLab/develop

Release 3.4.0

.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

.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 }}

.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

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`

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

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):
     """

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):
         """

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,

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',