vdjtools 2.2.1__tar.gz → 2.3.0__tar.gz

{vdjtools-2.2.1 → vdjtools-2.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vdjtools
-Version: 2.2.1
+Version: 2.3.0
 Summary: TCR/BCR repertoire analysis — Pgen/generation/inference, diversity, overlap, biomarkers (Python + C++)
 Keywords: immunology,tcr,bcr,airr,repertoire,pgen,olga,igor,bioinformatics
 Author-Email: Mikhail Shugay <mikhail.shugay@gmail.com>

{vdjtools-2.2.1 → vdjtools-2.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "scikit_build_core.build"
 
 [project]
 name = "vdjtools"  # if the PyPI name is taken, fall back to a distinct dist name (cf. arda -> arda-mapper)
-version = "2.2.1"
+version = "2.3.0"
 description = "TCR/BCR repertoire analysis — Pgen/generation/inference, diversity, overlap, biomarkers (Python + C++)"
 readme = "README.md"
 requires-python = ">=3.10"

{vdjtools-2.2.1 → vdjtools-2.3.0}/python/vdjtools/__init__.py

@@ -13,5 +13,5 @@ vdjmatch/seqtree) until a feature that needs them is used.
 """
 from ._core import hamming
 
-__version__ = "2.2.1"
+__version__ = "2.3.0"
 __all__ = ["hamming", "__version__"]

{vdjtools-2.2.1 → vdjtools-2.3.0}/python/vdjtools/model/__init__.py

@@ -8,7 +8,7 @@ OLGA's format with :func:`from_olga`; native models round-trip through :func:`sa
 from . import analyze
 from .bundled import list_bundled, load_bundled
 from .events import Event, EventKind
-from .io import from_olga, load_model, save_model
+from .io import from_arda, from_olga, load_model, save_model
 from .model import Model
 from .reference import cut_segment, load_germline, reconcile_olga, reverse_complement, translate
 from .schema import Manifest
@@ -21,6 +21,7 @@ __all__ = [
     "Manifest",
     "Model",
     "from_olga",
+    "from_arda",
     "load_model",
     "save_model",
     "load_bundled",

vdjtools-2.3.0/python/vdjtools/model/_bundled/arda/human_IGH/manifest.json

@@ -0,0 +1,88 @@
+{
+  "locus": "IGH",
+  "organism": "human",
+  "chain_type": "VDJ",
+  "model_version": "2.0.0",
+  "source": "arda:IGH+dd",
+  "error_rate": null,
+  "palindrome_max": {
+    "v_3": 4,
+    "d_5": 4,
+    "d_3": 4,
+    "j_5": 4
+  },
+  "events": {
+    "v_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "j_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "d_gene": {
+      "kind": "gene_choice",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "n_d": {
+      "kind": "n_d",
+      "given": []
+    },
+    "v_3_del": {
+      "kind": "deletion",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "j_5_del": {
+      "kind": "deletion",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "d_del": {
+      "kind": "deletion_2d",
+      "given": [
+        "d_gene"
+      ]
+    },
+    "vd_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "dj_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "vd_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    },
+    "dj_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    },
+    "d2_gene": {
+      "kind": "gene_choice",
+      "given": [
+        "d_gene"
+      ]
+    },
+    "d2_del": {
+      "kind": "deletion_2d",
+      "given": [
+        "d2_gene"
+      ]
+    },
+    "dd_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "dd_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    }
+  }
+}

vdjtools-2.3.0/python/vdjtools/model/_bundled/arda/human_IGK/manifest.json

@@ -0,0 +1,46 @@
+{
+  "locus": "IGK",
+  "organism": "human",
+  "chain_type": "VJ",
+  "model_version": "2.0.0",
+  "source": "arda:IGK",
+  "error_rate": null,
+  "palindrome_max": {
+    "v_3": 4,
+    "d_5": 4,
+    "d_3": 4,
+    "j_5": 4
+  },
+  "events": {
+    "v_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "j_choice": {
+      "kind": "gene_choice",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "v_3_del": {
+      "kind": "deletion",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "j_5_del": {
+      "kind": "deletion",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "vj_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "vj_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    }
+  }
+}

vdjtools-2.3.0/python/vdjtools/model/_bundled/arda/human_IGL/manifest.json

@@ -0,0 +1,46 @@
+{
+  "locus": "IGL",
+  "organism": "human",
+  "chain_type": "VJ",
+  "model_version": "2.0.0",
+  "source": "arda:IGL",
+  "error_rate": null,
+  "palindrome_max": {
+    "v_3": 4,
+    "d_5": 4,
+    "d_3": 4,
+    "j_5": 4
+  },
+  "events": {
+    "v_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "j_choice": {
+      "kind": "gene_choice",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "v_3_del": {
+      "kind": "deletion",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "j_5_del": {
+      "kind": "deletion",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "vj_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "vj_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    }
+  }
+}

vdjtools-2.3.0/python/vdjtools/model/_bundled/arda/human_TRA/manifest.json

@@ -0,0 +1,46 @@
+{
+  "locus": "TRA",
+  "organism": "human",
+  "chain_type": "VJ",
+  "model_version": "2.0.0",
+  "source": "arda:TRA",
+  "error_rate": null,
+  "palindrome_max": {
+    "v_3": 4,
+    "d_5": 4,
+    "d_3": 4,
+    "j_5": 4
+  },
+  "events": {
+    "v_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "j_choice": {
+      "kind": "gene_choice",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "v_3_del": {
+      "kind": "deletion",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "j_5_del": {
+      "kind": "deletion",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "vj_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "vj_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    }
+  }
+}

vdjtools-2.3.0/python/vdjtools/model/_bundled/arda/human_TRB/manifest.json

@@ -0,0 +1,88 @@
+{
+  "locus": "TRB",
+  "organism": "human",
+  "chain_type": "VDJ",
+  "model_version": "2.0.0",
+  "source": "arda:TRB+dd",
+  "error_rate": null,
+  "palindrome_max": {
+    "v_3": 4,
+    "d_5": 4,
+    "d_3": 4,
+    "j_5": 4
+  },
+  "events": {
+    "v_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "j_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "d_gene": {
+      "kind": "gene_choice",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "n_d": {
+      "kind": "n_d",
+      "given": []
+    },
+    "v_3_del": {
+      "kind": "deletion",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "j_5_del": {
+      "kind": "deletion",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "d_del": {
+      "kind": "deletion_2d",
+      "given": [
+        "d_gene"
+      ]
+    },
+    "vd_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "dj_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "vd_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    },
+    "dj_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    },
+    "d2_gene": {
+      "kind": "gene_choice",
+      "given": [
+        "d_gene"
+      ]
+    },
+    "d2_del": {
+      "kind": "deletion_2d",
+      "given": [
+        "d2_gene"
+      ]
+    },
+    "dd_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "dd_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    }
+  }
+}

vdjtools-2.3.0/python/vdjtools/model/_bundled/arda/human_TRD/manifest.json

@@ -0,0 +1,88 @@
+{
+  "locus": "TRD",
+  "organism": "human",
+  "chain_type": "VDJ",
+  "model_version": "2.0.0",
+  "source": "arda:TRD+dd",
+  "error_rate": null,
+  "palindrome_max": {
+    "v_3": 4,
+    "d_5": 4,
+    "d_3": 4,
+    "j_5": 4
+  },
+  "events": {
+    "v_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "j_choice": {
+      "kind": "gene_choice",
+      "given": []
+    },
+    "d_gene": {
+      "kind": "gene_choice",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "n_d": {
+      "kind": "n_d",
+      "given": []
+    },
+    "v_3_del": {
+      "kind": "deletion",
+      "given": [
+        "v_choice"
+      ]
+    },
+    "j_5_del": {
+      "kind": "deletion",
+      "given": [
+        "j_choice"
+      ]
+    },
+    "d_del": {
+      "kind": "deletion_2d",
+      "given": [
+        "d_gene"
+      ]
+    },
+    "vd_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "dj_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "vd_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    },
+    "dj_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    },
+    "d2_gene": {
+      "kind": "gene_choice",
+      "given": [
+        "d_gene"
+      ]
+    },
+    "d2_del": {
+      "kind": "deletion_2d",
+      "given": [
+        "d2_gene"
+      ]
+    },
+    "dd_ins": {
+      "kind": "ins_length",
+      "given": []
+    },
+    "dd_dinucl": {
+      "kind": "dinucleotide",
+      "given": []
+    }
+  }
+}