feat: Save cached files to evidence_matching folder (#296)

Author: jarbesfeld

notebooks/evidence_matching/civic_cache.pkl

@@ -208,7 +208,8 @@
      "output_type": "stream",
      "text": [
       "WARNING:cool_seq_tool.mappers.exon_genomic_coords:48406078 on NC_000023.11 occurs more than 150 bp outside the exon boundaries of the NM_005636.4 transcript, indicating this may not be a chimeric transcript junction and is unlikely to represent a contiguous coding sequence. Confirm that the genomic position 48406078 is being used to represent transcript junction and not DNA breakpoint.\n",
-      "WARNING:fusor.harvester:15 fusion(s) were dropped during translation\n"
+      "WARNING:fusor.harvester:15 fusion(s) were dropped during translation\n",
+      "WARNING:fusor.models:Cached fusions file already exists. Overwriting with new file\n"
      ]
     },
     {
@@ -228,7 +229,7 @@
     "from fusor.models import save_fusions_cache\n",
     "\n",
     "# Generate categorical fusions list\n",
-    "harvester = CIVICHarvester(fusor=fusor)\n",
+    "harvester = CIVICHarvester(fusor=fusor, local_cache_path=\"civic_cache.pkl\")\n",
     "harvester.fusions_list = variants\n",
     "civic_fusions = await harvester.load_records()\n",
     "\n",
@@ -532,24 +533,17 @@
    "id": "92b5485c",
    "metadata": {},
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Downloading v.2025-06-12.zip...\n"
-     ]
-    },
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "519kB [00:00, 4.56MB/s]\n"
+      "WARNING:fusor.models:Cached fusions file already exists. Overwriting with new file\n"
      ]
     }
    ],
    "source": [
     "from fusor.harvester import MOAHarvester\n",
-    "harvester = MOAHarvester(fusor=fusor, cache_dir=config.data_root)\n",
+    "harvester = MOAHarvester(fusor=fusor, cache_dir=Path.cwd())\n",
     "moa_fusions = harvester.load_records()\n",
     "\n",
     "# Save cache for later\n",