Skip to content

Commit

Permalink
WWOX update
Browse files Browse the repository at this point in the history
  • Loading branch information
@pnrobinson
pnrobinson committed Jan 12, 2025
1 parent 8c175e6 commit c84fb2c
Show file tree
Hide file tree
Showing 41 changed files with 109 additions and 122 deletions.
20 changes: 10 additions & 10 deletions notebooks/WWOX/WWOX_DEE28_individuals.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,15 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 3,
"id": "e5d196a5-0eea-4172-8e54-e1b0cbcd7d21",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using pyphetools version 0.9.113\n"
"Using pyphetools version 0.9.115\n"
]
}
],
Expand All @@ -32,7 +32,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 4,
"id": "6fbeec2a-08f4-409a-80f7-60fe62e5c626",
"metadata": {},
"outputs": [],
Expand All @@ -44,7 +44,7 @@
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 9,
"id": "5a7789fc",
"metadata": {},
"outputs": [
Expand All @@ -60,15 +60,15 @@
}
],
"source": [
"dels = {\"DEL exon 1-5\" , \"DEL exon 6-8\", \"DEL 2.8 Mb\"}\n",
"\n",
"dels = {\"DEL:exon 1-5\" , \"DEL:exon 6-8\",\"DEL:2.8 Mb\" }\n",
"dups = {\"DUP:exon 6-8\"}\n",
"timporter = TemplateImporter(template=template, hp_json=hp_json, created_by=created_by)\n",
"individual_list, cvalidator = timporter.import_phenopackets_from_template(deletions=dels)"
"individual_list, cvalidator = timporter.import_phenopackets_from_template(deletions=dels, duplications=dups)"
]
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 10,
"id": "56ee298e-10fa-445e-8349-5ab11d8dedad",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -100,7 +100,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 11,
"id": "5d044b78",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -368,7 +368,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.8"
}
},
"nbformat": 4,
Expand Down
83 changes: 41 additions & 42 deletions notebooks/WWOX/WWOX_SCAR12_individuals.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,15 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 1,
"id": "ec2afcb4-cf50-40fe-b4f0-9c1f878b6aa2",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using pyphetools version 0.9.113\n"
"Using pyphetools version 0.9.115\n"
]
}
],
Expand All @@ -33,41 +33,40 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 2,
"id": "70c1eb70-61a8-4d38-aa13-0c457f3523d7",
"metadata": {},
"outputs": [],
"source": [
"template = \"input/WWOX_SCAR12_individuals.xlsx\"\n",
"hp_json = \"../hp.json\"\n",
"created_by = \"0000-0002-0736-9199\""
]
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 3,
"id": "5a7789fc",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HPO version 2024-08-13\n",
"HPO version 2024-12-12\n",
"Created encoders for 29 fields\n",
"Importing OMIM:614322, Spinocerebellar ataxia, autosomal recessive 12, HGNC:12799, WWOX, NM_016373.2\n",
"We output 6 GA4GH phenopackets to the directory phenopackets\n"
]
}
],
"source": [
"timporter = TemplateImporter(template=template, hp_json=hp_json, created_by=created_by)\n",
"timporter = TemplateImporter(template=template, created_by=created_by)\n",
"individual_list, cvalidator = timporter.import_phenopackets_from_template()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 4,
"id": "f17c3924",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -98,7 +97,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 5,
"id": "fd367ed6",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -131,7 +130,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 6,
"id": "23f1094f",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -201,7 +200,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
Expand All @@ -218,7 +217,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
Expand All @@ -235,7 +234,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
Expand All @@ -252,7 +251,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
Expand All @@ -269,7 +268,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
Expand All @@ -286,7 +285,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
Expand All @@ -303,7 +302,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
Expand All @@ -320,7 +319,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
Expand All @@ -337,7 +336,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
Expand All @@ -354,7 +353,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
Expand All @@ -371,7 +370,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
Expand All @@ -388,7 +387,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
Expand All @@ -405,7 +404,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
Expand All @@ -422,7 +421,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
Expand All @@ -439,7 +438,7 @@
" <td></td>\n",
" <td>PMID:24369382</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-11-12]</td>\n",
" <td>ORCID:0000-0002-0736-9199[2025-01-12]</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
Expand Down Expand Up @@ -498,24 +497,24 @@
"14 PMID:24369382 PCS \n",
"\n",
" biocuration \n",
"0 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"1 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"2 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"3 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"4 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"5 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"6 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"7 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"8 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"9 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"10 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"11 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"12 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"13 ORCID:0000-0002-0736-9199[2024-11-12] \n",
"14 ORCID:0000-0002-0736-9199[2024-11-12] "
"0 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"1 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"2 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"3 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"4 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"5 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"6 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"7 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"8 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"9 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"10 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"11 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"12 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"13 ORCID:0000-0002-0736-9199[2025-01-12] \n",
"14 ORCID:0000-0002-0736-9199[2025-01-12] "
]
},
"execution_count": 12,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -550,7 +549,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
"version": "3.12.8"
}
},
"nbformat": 4,
Expand Down
Binary file modified notebooks/WWOX/input/WWOX_DEE28_individuals.xlsx
View file
Binary file not shown.
4 changes: 2 additions & 2 deletions notebooks/WWOX/phenopackets/PMID_24369382_Family1II1.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,7 @@
}
],
"metaData": {
"created": "2024-11-12T08:04:44.274138927Z",
"created": "2025-01-12T18:26:19.503175020Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
Expand Down Expand Up @@ -169,7 +169,7 @@
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2024-08-13",
"version": "2024-12-12",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
Expand Down
4 changes: 2 additions & 2 deletions notebooks/WWOX/phenopackets/PMID_24369382_Family1II2.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@
}
],
"metaData": {
"created": "2024-11-12T08:04:44.274778127Z",
"created": "2025-01-12T18:26:19.504307985Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
Expand Down Expand Up @@ -175,7 +175,7 @@
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2024-08-13",
"version": "2024-12-12",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
Expand Down
4 changes: 2 additions & 2 deletions notebooks/WWOX/phenopackets/PMID_24369382_Family1II3.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@
}
],
"metaData": {
"created": "2024-11-12T08:04:44.275202035Z",
"created": "2025-01-12T18:26:19.504781007Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
Expand Down Expand Up @@ -175,7 +175,7 @@
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2024-08-13",
"version": "2024-12-12",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
Expand Down
Loading

0 comments on commit c84fb2c

Please sign in to comment.