diff --git a/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb b/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb index e54dd518..f98abf2c 100644 --- a/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb +++ b/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb @@ -169,9 +169,9 @@ { "data": { "text/plain": [ - "{'id': 'ga4gh:CX.XQt04FoCIptvgp6GtE2qjEaUJC7cr1wo',\n", + "{'id': 'ga4gh:CX.SlJJkuXM8b0b63ADyDMxV-MpLBi7BhfI',\n", " 'type': 'CopyNumberChange',\n", - " 'digest': 'XQt04FoCIptvgp6GtE2qjEaUJC7cr1wo',\n", + " 'digest': 'SlJJkuXM8b0b63ADyDMxV-MpLBi7BhfI',\n", " 'location': {'id': 'ga4gh:SL.GSJAEJXFDz7Nq6VlJj5NTEku48MmteUU',\n", " 'type': 'SequenceLocation',\n", " 'digest': 'GSJAEJXFDz7Nq6VlJj5NTEku48MmteUU',\n", @@ -179,7 +179,7 @@ " 'refgetAccession': 'SQ.eK4D2MosgK_ivBkgi6FVPg5UXs1bYESm'},\n", " 'start': 45002866,\n", " 'end': 45015056},\n", - " 'copyChange': 'EFO:0030067'}" + " 'copyChange': 'loss'}" ] }, "execution_count": 4, @@ -189,7 +189,7 @@ ], "source": [ "cnv_translator = CnvTranslator(data_proxy=seqrepo_dataproxy)\n", - "cnc = cnv_translator.translate_from(\"NC_000014.9:g.45002867_45015056del\", \"hgvs\", copy_change=\"EFO:0030067\")\n", + "cnc = cnv_translator.translate_from(\"NC_000014.9:g.45002867_45015056del\", \"hgvs\", copy_change=\"loss\")\n", "cnc.model_dump(exclude_none=True)" ] }, @@ -208,7 +208,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "id": "f4efc189d53d7000", "metadata": { "ExecuteTime": { @@ -224,9 +224,9 @@ { "data": { "text/plain": [ - "{'id': 'ga4gh:CX.3eGz_p3ufUDGtk87RYBI22dfihLInCOa',\n", + "{'id': 'ga4gh:CX.jPS3b_jC01NchtIA13jc6bSGgxE0UTkt',\n", " 'type': 'CopyNumberChange',\n", - " 'digest': '3eGz_p3ufUDGtk87RYBI22dfihLInCOa',\n", + " 'digest': 'jPS3b_jC01NchtIA13jc6bSGgxE0UTkt',\n", " 'location': {'id': 'ga4gh:SL.tydo6UFL8Y60L5Me3k8AJfljURO9vYn9',\n", " 'type': 'SequenceLocation',\n", " 'digest': 'tydo6UFL8Y60L5Me3k8AJfljURO9vYn9',\n", @@ -234,16 +234,16 @@ " 'refgetAccession': 'SQ.KEO-4XBcm1cxeo_DIQ8_ofqGUkp4iZhI'},\n", " 'start': 75502957,\n", " 'end': 76045032},\n", - " 'copyChange': 'EFO:0030070'}" + " 'copyChange': 'gain'}" ] }, - "execution_count": 6, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "cnx = cnv_translator.translate_from(\"NC_000009.12:g.75502958_76045032dup\", \"hgvs\", copy_change=\"EFO:0030070\")\n", + "cnx = cnv_translator.translate_from(\"NC_000009.12:g.75502958_76045032dup\", \"hgvs\", copy_change=\"gain\")\n", "cnx.model_dump(exclude_none=True)" ] }, @@ -275,7 +275,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 6, "id": "f057e93172e97a88", "metadata": { "ExecuteTime": { @@ -304,7 +304,7 @@ " 'copies': 3}" ] }, - "execution_count": 7, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -329,7 +329,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 7, "id": "412feaeba95751e7", "metadata": { "ExecuteTime": { @@ -358,7 +358,7 @@ " 'copies': 1}" ] }, - "execution_count": 8, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -371,7 +371,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "vrs-python (3.12.11)", "language": "python", "name": "python3" }, @@ -385,7 +385,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.1" + "version": "3.12.11" } }, "nbformat": 4, diff --git a/notebooks/getting_started/6_Upcoming_features.ipynb b/notebooks/getting_started/6_Upcoming_features.ipynb index 0100bb9e..54bef10c 100644 --- a/notebooks/getting_started/6_Upcoming_features.ipynb +++ b/notebooks/getting_started/6_Upcoming_features.ipynb @@ -293,14 +293,15 @@ "text/plain": [ "{'id': None,\n", " 'type': 'SequenceReference',\n", - " 'label': None,\n", + " 'name': None,\n", " 'description': None,\n", - " 'alternativeLabels': None,\n", + " 'aliases': None,\n", " 'extensions': None,\n", - " 'mappings': None,\n", " 'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI',\n", " 'residueAlphabet': None,\n", - " 'circular': None}" + " 'circular': None,\n", + " 'sequence': None,\n", + " 'moleculeType': None}" ] }, "execution_count": 7, @@ -399,8 +400,8 @@ "text/plain": [ "{'id': 'refseq:NC_000005.10',\n", " 'type': 'SequenceReference',\n", - " 'label': 'GRCh38:5',\n", - " 'alternativeLabels': ['GRCh38:chr5'],\n", + " 'name': 'GRCh38:chr5',\n", + " 'aliases': ['GRCh38:5'],\n", " 'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'}" ] }, @@ -411,8 +412,8 @@ ], "source": [ "seqref.id = seqrepo_dataproxy.translate_sequence_identifier(ref_namespaced_id, \"refseq\")[0]\n", - "seqref.label = seqrepo_dataproxy.translate_sequence_identifier(ref_namespaced_id, \"GRCh38\")[0]\n", - "seqref.alternativeLabels = seqrepo_dataproxy.translate_sequence_identifier(ref_namespaced_id, \"GRCh38\")[1:]\n", + "seqref.name = seqrepo_dataproxy.translate_sequence_identifier(ref_namespaced_id, \"GRCh38\")[0]\n", + "seqref.aliases = seqrepo_dataproxy.translate_sequence_identifier(ref_namespaced_id, \"GRCh38\")[1:]\n", "seqref.model_dump(exclude_none=True)" ] }, @@ -438,8 +439,8 @@ " 'digest': 'nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n", " 'sequenceReference': {'id': 'refseq:NC_000005.10',\n", " 'type': 'SequenceReference',\n", - " 'label': 'GRCh38:5',\n", - " 'alternativeLabels': ['GRCh38:chr5'],\n", + " 'name': 'GRCh38:chr5',\n", + " 'aliases': ['GRCh38:5'],\n", " 'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'},\n", " 'start': 80656509,\n", " 'end': 80656510}" @@ -471,8 +472,8 @@ " 'digest': 'nA5-KovovkH-5p3LF1657nkkeWFwrInI',\n", " 'sequenceReference': {'id': 'refseq:NC_000005.10',\n", " 'type': 'SequenceReference',\n", - " 'label': 'GRCh38:5',\n", - " 'alternativeLabels': ['GRCh38:chr5'],\n", + " 'name': 'GRCh38:chr5',\n", + " 'aliases': ['GRCh38:5'],\n", " 'refgetAccession': 'SQ.aUiQCzCPZ2d0csHbMSbh2NzInhonSXwI'},\n", " 'start': 80656509,\n", " 'end': 80656510},\n", @@ -491,7 +492,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Python 3 (ipykernel)", + "display_name": "vrs-python (3.12.11)", "language": "python", "name": "python3" }, @@ -505,7 +506,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.2" + "version": "3.12.11" } }, "nbformat": 4,