Merge branch 'develop' into 'master'

Release v0.6.1 See merge request tron/addannot!196
TRON-Bioinformatics · Feb 8, 2022 · a83c4be · a83c4be
2 parents ed32e53 + 4edb733
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diff --git a/MANIFEST.in b/MANIFEST.in
@@ -11,4 +11,6 @@ include neofox/published_features/hex/EPItOMe_modified.R
 include neofox/published_features/hex/hex.R
 include neofox/expression_imputation/tcga_cohort_code.tab
 include neofox/expression_imputation/tcga_exp_summary_modified.tab.gz.tbi
-include neofox/expression_imputation/tcga_exp_summary_modified.tab.gz
+include neofox/expression_imputation/tcga_exp_summary_modified.tab.gz
+include requirements.txt
+include README.md
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,9 +2,9 @@ Sphinx==4.2.0
 m2r2==0.3.1
 nbsphinx==0.8.7
 pandoc==1.1.0
-ipython==7.16.1
+ipython==8.0.1
 ipykernel==5.3.4
 #sphinx_rtd_theme==0.5.0
 #insipid_sphinx_theme==0.2.1
 pydata-sphinx-theme==0.7.1
-Jinja2==2.11
+Jinja2==3.0.3
diff --git a/docs/source/03_03_usage.md b/docs/source/03_03_usage.md
@@ -7,7 +7,11 @@ There are two ways to use NeoFox for annotation of neoantigen candidates with ne
 To call NeoFox from the command line, use the following command. Make sure that the requirements have been added to PATH as described [here](02_installation.md) or add a config file as described below:  
 
 ````commandline
-neofox --candidate-file/--json-file neoantigens_candidates.tab/neoantigens_candidates.json --patient-data patient_data.txt --output-folder /path/to/out --output-prefix out_prefix  [--with-table] [--with-json] [--num_cpus] [--affinity-threshold] [--config] [--patient-id]
+neofox --candidate-file/--json-file neoantigens_candidates.tab/neoantigens_candidates.json \
+    --patient-data patient_data.txt \
+    --output-folder /path/to/out \
+    --output-prefix out_prefix  \
+    [--with-table] [--with-json] [--num_cpus] [--affinity-threshold] [--config] [--patient-id]
 ````
 
 where:
@@ -34,7 +38,10 @@ where:
 This is an example to call NeoFox with a candidate-file and obtaining the annotated neoantigen candidates in [tabular](03_02_output_data.md#tabular-format) format:  
 
 ````commandline
-neofox --candidate-file neoantigens_candidates.tab --patient-data patient_data.tab --output-folder /path/to/out --output-prefix test
+neofox --candidate-file neoantigens_candidates.tab \
+    --patient-data patient_data.tab \
+    --output-folder /path/to/out \
+    --output-prefix test
 ````
 
 The optional **config** file with the paths to the dependencies can look like this:  

diff --git a/docs/source/03_04_examples.md b/docs/source/03_04_examples.md
@@ -1,10 +1,5 @@
 # Examples
 
-## Notebooks 
-
-- :ref:`/notebooks/api_usage.ipynb`
-
-
 ## Demo dataset
 
 - :download:`Neoantigens input file </notebooks/test_model_file.txt>`

diff --git a/docs/source/notebooks/api_usage.ipynb b/docs/source/notebooks/api_usage.ipynb
@@ -26,7 +26,7 @@
     {
      "data": {
       "text/plain": [
-       "'0.5.4.dev3'"
+       "'0.6.1'"
       ]
      },
      "execution_count": 1,
@@ -55,53 +55,32 @@
     "### Create a neoantigen\n"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from neofox.model.neoantigen import Neoantigen, Mutation"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Create a mutation:"
+    "Create a neoantigen candidate:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "mutation = Mutation(\n",
-    "    wild_type_xmer=\"DEVLGEPSQDILVIDQTRLEATISPET\", \n",
-    "    mutated_xmer=\"DEVLGEPSQDILVTDQTRLEATISPET\")"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Create a neoantigen using the previous transcript and mutation:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
-    "neoantigen = Neoantigen(\n",
+    "from neofox.model.factories import NeoantigenFactory\n",
+    "\n",
+    "# create a neoantigen candidate using the factory\n",
+    "neoantigen = NeoantigenFactory.build_neoantigen(\n",
+    "    mutated_xmer=\"DEVLGEPSQDILVTDQTRLEATISPET\",\n",
+    "    wild_type_xmer=\"DEVLGEPSQDILVIDQTRLEATISPET\",\n",
     "    patient_identifier=\"P123\", \n",
-    "    mutation=mutation, \n",
-    "    gene=\"VCAN\", \n",
+    "    gene=\"VCAN\",\n",
     "    rna_expression=0.519506894, \n",
     "    rna_variant_allele_frequency=0.857142857, \n",
-    "    dna_variant_allele_frequency=0.294573643)"
+    "    dna_variant_allele_frequency=0.294573643,\n",
+    "    my_custom_annotation=\"add any custom annotation as additional fields with any name\"\n",
+    ")"
    ]
   },
   {
@@ -119,7 +98,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
@@ -130,12 +109,22 @@
       "  \"patientIdentifier\": \"P123\",\n",
       "  \"gene\": \"VCAN\",\n",
       "  \"mutation\": {\n",
+      "    \"position\": [\n",
+      "      14\n",
+      "    ],\n",
       "    \"wildTypeXmer\": \"DEVLGEPSQDILVIDQTRLEATISPET\",\n",
       "    \"mutatedXmer\": \"DEVLGEPSQDILVTDQTRLEATISPET\"\n",
       "  },\n",
       "  \"rnaExpression\": 0.519506894,\n",
+      "  \"imputedGeneExpression\": null,\n",
       "  \"dnaVariantAlleleFrequency\": 0.294573643,\n",
-      "  \"rnaVariantAlleleFrequency\": 0.857142857\n",
+      "  \"rnaVariantAlleleFrequency\": 0.857142857,\n",
+      "  \"externalAnnotations\": [\n",
+      "    {\n",
+      "      \"name\": \"my_custom_annotation\",\n",
+      "      \"value\": \"add any custom annotation as additional fields with any name\"\n",
+      "    }\n",
+      "  ]\n",
       "}\n"
      ]
     }
@@ -153,22 +142,26 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
        "{'patientIdentifier': 'P123',\n",
        " 'gene': 'VCAN',\n",
-       " 'mutation': {'wildTypeXmer': 'DEVLGEPSQDILVIDQTRLEATISPET',\n",
+       " 'mutation': {'position': [14],\n",
+       "  'wildTypeXmer': 'DEVLGEPSQDILVIDQTRLEATISPET',\n",
        "  'mutatedXmer': 'DEVLGEPSQDILVTDQTRLEATISPET'},\n",
        " 'rnaExpression': 0.519506894,\n",
+       " 'imputedGeneExpression': None,\n",
        " 'dnaVariantAlleleFrequency': 0.294573643,\n",
-       " 'rnaVariantAlleleFrequency': 0.857142857}"
+       " 'rnaVariantAlleleFrequency': 0.857142857,\n",
+       " 'externalAnnotations': [{'name': 'my_custom_annotation',\n",
+       "   'value': 'add any custom annotation as additional fields with any name'}]}"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -186,16 +179,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "b'\\n\\x04P123\\x12\\x04VCAN\\x1a:\\x12\\x1bDEVLGEPSQDILVIDQTRLEATISPET\\x1a\\x1bDEVLGEPSQDILVTDQTRLEATISPET%g\\xfe\\x04?5[\\xd2\\x96>=\\xb7m[?'"
+       "b'\\n\\x04P123\\x12\\x04VCAN\\x1a=\\n\\x01\\x0e\\x12\\x1bDEVLGEPSQDILVIDQTRLEATISPET\\x1a\\x1bDEVLGEPSQDILVTDQTRLEATISPET%g\\xfe\\x04?5[\\xd2\\x96>=\\xb7m[?JT\\n\\x14my_custom_annotation\\x12<add any custom annotation as additional fields with any name'"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -217,57 +210,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
     "import pandas as pd\n",
     "from neofox.model.conversion import ModelConverter"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Transform a neoantigen into a Pandas `Series`:"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "patient_identifier                                             P123\n",
-       "gene                                                           VCAN\n",
-       "rna_expression                                             0.519507\n",
-       "imputed_gene_expression                                           0\n",
-       "dna_variant_allele_frequency                               0.294574\n",
-       "rna_variant_allele_frequency                               0.857143\n",
-       "external_annotations                                             []\n",
-       "mutation.position                                                []\n",
-       "mutation.wild_type_xmer                 DEVLGEPSQDILVIDQTRLEATISPET\n",
-       "mutation.mutated_xmer                   DEVLGEPSQDILVTDQTRLEATISPET\n",
-       "neofox_annotations.annotations                                   []\n",
-       "neofox_annotations.annotator                                       \n",
-       "neofox_annotations.annotator_version                               \n",
-       "neofox_annotations.timestamp                                       \n",
-       "neofox_annotations.resources_hash                                  \n",
-       "Name: 0, dtype: object"
-      ]
-     },
-     "execution_count": 9,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "neoantigen_series = ModelConverter.object2series(neoantigen)\n",
-    "neoantigen_series"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -499,7 +449,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -516,14 +466,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "[E 210928 12:18:02 validation:85] {}\n"
+      "[E 220208 11:32:29 validation:86] {}\n"
      ]
     },
     {
@@ -535,6 +485,8 @@
     }
    ],
    "source": [
+    "from neofox.model.neoantigen import Neoantigen, Mutation\n",
+    "\n",
     "try:\n",
     "    ModelValidator.validate_neoantigen(neoantigen=Neoantigen())\n",
     "except NeofoxDataValidationException as e:\n",
@@ -557,13 +509,20 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "[E 210928 12:18:02 validation:85] {\n",
+      "[E 220208 11:59:28 validation:86] {\n",
       "       \"patientIdentifier\": \"12345\",\n",
       "       \"gene\": \"VCAN\",\n",
       "       \"mutation\": {\n",
-      "          \"wildTypeXmer\": \"123456AAAAAAAAAAAAAA\",\n",
-      "          \"mutatedXmer\": \"123456GAAAAAAAAAAAAA\"\n",
-      "       }\n",
+      "          \"position\": [\n",
+      "             7\n",
+      "          ],\n",
+      "          \"wildTypeXmer\": \"123456GAAAAAAAAAAAAA\",\n",
+      "          \"mutatedXmer\": \"123456AAAAAAAAAAAAAA\"\n",
+      "       },\n",
+      "       \"rnaExpression\": null,\n",
+      "       \"imputedGeneExpression\": null,\n",
+      "       \"dnaVariantAlleleFrequency\": null,\n",
+      "       \"rnaVariantAlleleFrequency\": null\n",
       "    }\n"
      ]
     },
@@ -577,12 +536,11 @@
    ],
    "source": [
     "try:\n",
-    "    ModelValidator.validate_neoantigen(neoantigen=Neoantigen(\n",
+    "    NeoantigenFactory.build_neoantigen(\n",
     "        patient_identifier=\"12345\",\n",
     "        gene=\"VCAN\",\n",
-    "        mutation=Mutation(\n",
-    "            wild_type_xmer=\"123456AAAAAAAAAAAAAA\", # wrong aminoacid representation\n",
-    "            mutated_xmer=\"123456GAAAAAAAAAAAAA\")))\n",
+    "        mutated_xmer=\"123456AAAAAAAAAAAAAA\", # wrong aminoacid representation\n",
+    "        wild_type_xmer=\"123456GAAAAAAAAAAAAA\")\n",
     "except NeofoxDataValidationException as e:\n",
     "    print(\"Error message: {}\".format(e))"
    ]
@@ -605,7 +563,17 @@
      "text": [
       "{\n",
       "  \"position\": [\n",
-      "    6\n",
+      "    1,\n",
+      "    2,\n",
+      "    3,\n",
+      "    4,\n",
+      "    5,\n",
+      "    6,\n",
+      "    7,\n",
+      "    8,\n",
+      "    9,\n",
+      "    10,\n",
+      "    11\n",
       "  ],\n",
       "  \"wildTypeXmer\": \"AAAAAAAAAAAAA\",\n",
       "  \"mutatedXmer\": \"AAAAAGAAAAA\"\n",
@@ -614,11 +582,10 @@
     }
    ],
    "source": [
-    "valid_neoantigen = ModelValidator.validate_neoantigen(neoantigen=Neoantigen(\n",
+    "valid_neoantigen = NeoantigenFactory.build_neoantigen(\n",
     "    patient_identifier=\"12345\",\n",
-    "    mutation=Mutation(\n",
-    "        wild_type_xmer=\"AAAAAAAAAAAAA\",\n",
-    "        mutated_xmer=\"aaaaaGaaaaa\")))\n",
+    "    wild_type_xmer=\"AAAAAAAAAAAAA\",\n",
+    "    mutated_xmer=\"aaaaaGaaaaa\")\n",
     "\n",
     "print(valid_neoantigen.mutation.to_json(indent=2))"
    ]

diff --git a/neofox/__init__.py b/neofox/__init__.py
@@ -16,7 +16,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.#
-VERSION = "0.6.0"
+VERSION = "0.6.1"
 
 
 REFERENCE_FOLDER_ENV = "NEOFOX_REFERENCE_FOLDER"