chore!: remove localizer (#379)

* remove localizer
ga4gh · Apr 4, 2024 · e057610 · e057610
1 parent 69d3ed3
commit e057610
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diff --git a/notebooks/ChromosomeLocation.ipynb b/notebooks/ChromosomeLocation.ipynb
@@ -112,46 +112,6 @@
     "ga4gh_identify(cbl)"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### Localization"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from ga4gh.vrs.extras.localizer import Localizer\n",
-    "lr = Localizer()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'GRCh37': {'sequence_id': 'refseq:NC_000011.9',\n",
-       "  'interval': {'start': {'value': 102100000}, 'end': {'value': 110400000}}},\n",
-       " 'GRCh38': {'sequence_id': 'refseq:NC_000011.10',\n",
-       "  'interval': {'start': {'value': 102300000}, 'end': {'value': 110600000}}}}"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "{assy: lr.localize_named_feature(cbl, assy).as_dict() for assy in (\"GRCh37\", \"GRCh38\")}"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -176,7 +136,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.10"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/notebooks/Feature Based Locations.ipynb b/notebooks/Feature Based Locations.ipynb
@@ -58,8 +58,8 @@
     }
    ],
    "source": [
-    "cbl1 = models.ChromosomeLocation(species_id=\"taxonomy:9606\", \n",
-    "                                 chr=\"11\", \n",
+    "cbl1 = models.ChromosomeLocation(species_id=\"taxonomy:9606\",\n",
+    "                                 chr=\"11\",\n",
     "                                 interval=models.CytobandInterval(start=\"q22.2\", end=\"q22.3\", type=\"CytobandInterval\"),\n",
     "                                 type=\"ChromosomeLocation\"\n",
     "                                )\n",
@@ -113,61 +113,6 @@
     "ga4gh_identify(cbl1)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "## Localization\n",
-    "from ga4gh.vrs.extras.localizer import Localizer\n",
-    "lr = Localizer()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'sequence_id': 'refseq:NC_000011.9',\n",
-       " 'interval': {'start': {'value': 102100000}, 'end': {'value': 110400000}}}"
-      ]
-     },
-     "execution_count": 6,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "cbl1sl37 = lr.localize_named_feature(cbl1, \"GRCh37\")\n",
-    "cbl1sl37.as_dict()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "{'sequence_id': 'refseq:NC_000011.10',\n",
-       " 'interval': {'start': {'value': 102300000}, 'end': {'value': 110600000}}}"
-      ]
-     },
-     "execution_count": 7,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "cbl1sl38 = lr.localize_named_feature(cbl1, \"GRCh38\")\n",
-    "cbl1sl38.as_dict()"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -192,7 +137,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.10"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/src/ga4gh/vrs/extras/localizer.py b/src/ga4gh/vrs/extras/localizer.py