From 289a4c423b93aa4e9788bf77835f69df83c0f89f Mon Sep 17 00:00:00 2001
From: "Alex H. Wagner, PhD" <Alex.Wagner@nationwidechildrens.org>
Date: Wed, 17 Jul 2024 10:47:44 -0400
Subject: [PATCH] rename variable from allele to cnc or cnx

---
 .../5_Exploring_the_CnvTranslator.ipynb       | 44 +++++++++----------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb b/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb
index 0af84722..44252c7a 100644
--- a/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb
+++ b/notebooks/getting_started/5_Exploring_the_CnvTranslator.ipynb
@@ -170,16 +170,16 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CX.0M5VkV5v504_laQURFMEsqzZGcOF9YEw',\n",
-       " 'type': 'CopyNumberChange',\n",
+       " 'type': <VrsType.CN_CHANGE: 'CopyNumberChange'>,\n",
        " 'digest': '0M5VkV5v504_laQURFMEsqzZGcOF9YEw',\n",
        " 'location': {'id': 'ga4gh:SL.GSJAEJXFDz7Nq6VlJj5NTEku48MmteUU',\n",
-       "  'type': 'SequenceLocation',\n",
+       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
        "  'digest': 'GSJAEJXFDz7Nq6VlJj5NTEku48MmteUU',\n",
-       "  'sequenceReference': {'type': 'SequenceReference',\n",
+       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
        "   'refgetAccession': 'SQ.eK4D2MosgK_ivBkgi6FVPg5UXs1bYESm'},\n",
        "  'start': 45002866,\n",
        "  'end': 45015056},\n",
-       " 'copyChange': 'efo:0030067'}"
+       " 'copyChange': <CopyChange.EFO_0030067: 'efo:0030067'>}"
       ]
      },
      "execution_count": 4,
@@ -189,8 +189,8 @@
    ],
    "source": [
     "cnv_translator = CnvTranslator(data_proxy=seqrepo_dataproxy)\n",
-    "allele = cnv_translator.translate_from(\"NC_000014.9:g.45002867_45015056del\", \"hgvs\", copy_change=\"efo:0030067\")\n",
-    "allele.model_dump(exclude_none=True)"
+    "cnc = cnv_translator.translate_from(\"NC_000014.9:g.45002867_45015056del\", \"hgvs\", copy_change=\"efo:0030067\")\n",
+    "cnc.model_dump(exclude_none=True)"
    ]
   },
   {
@@ -225,16 +225,16 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CX.0BN4vrqPrLPAZYsQEAPnG4IS8AYeBGe1',\n",
-       " 'type': 'CopyNumberChange',\n",
+       " 'type': <VrsType.CN_CHANGE: 'CopyNumberChange'>,\n",
        " 'digest': '0BN4vrqPrLPAZYsQEAPnG4IS8AYeBGe1',\n",
        " 'location': {'id': 'ga4gh:SL.tydo6UFL8Y60L5Me3k8AJfljURO9vYn9',\n",
-       "  'type': 'SequenceLocation',\n",
+       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
        "  'digest': 'tydo6UFL8Y60L5Me3k8AJfljURO9vYn9',\n",
-       "  'sequenceReference': {'type': 'SequenceReference',\n",
+       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
        "   'refgetAccession': 'SQ.KEO-4XBcm1cxeo_DIQ8_ofqGUkp4iZhI'},\n",
        "  'start': 75502957,\n",
        "  'end': 76045032},\n",
-       " 'copyChange': 'efo:0030070'}"
+       " 'copyChange': <CopyChange.EFO_0030070: 'efo:0030070'>}"
       ]
      },
      "execution_count": 5,
@@ -243,8 +243,8 @@
     }
    ],
    "source": [
-    "allele = cnv_translator.translate_from(\"NC_000009.12:g.75502958_76045032dup\", \"hgvs\", copy_change=\"efo:0030070\")\n",
-    "allele.model_dump(exclude_none=True)"
+    "cnx = cnv_translator.translate_from(\"NC_000009.12:g.75502958_76045032dup\", \"hgvs\", copy_change=\"efo:0030070\")\n",
+    "cnx.model_dump(exclude_none=True)"
    ]
   },
   {
@@ -292,12 +292,12 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CN.O_QHImmfErh9jDFkJaypPPvUmnj7EM70',\n",
-       " 'type': 'CopyNumberCount',\n",
+       " 'type': <VrsType.CN_COUNT: 'CopyNumberCount'>,\n",
        " 'digest': 'O_QHImmfErh9jDFkJaypPPvUmnj7EM70',\n",
        " 'location': {'id': 'ga4gh:SL.hBVWalem_rNclxjmUuT9CHbEGCdlqW9L',\n",
-       "  'type': 'SequenceLocation',\n",
+       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
        "  'digest': 'hBVWalem_rNclxjmUuT9CHbEGCdlqW9L',\n",
-       "  'sequenceReference': {'type': 'SequenceReference',\n",
+       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
        "   'refgetAccession': 'SQ.HxuclGHh0XCDuF8x6yQrpHUBL7ZntAHc'},\n",
        "  'start': 85623,\n",
        "  'end': 57073230},\n",
@@ -310,8 +310,8 @@
     }
    ],
    "source": [
-    "allele = cnv_translator.translate_from(\"NC_000004.12:g.85624_57073230dup\", \"hgvs\", copies=\"3\")\n",
-    "allele.model_dump(exclude_none=True)"
+    "cnc = cnv_translator.translate_from(\"NC_000004.12:g.85624_57073230dup\", \"hgvs\", copies=\"3\")\n",
+    "cnc.model_dump(exclude_none=True)"
    ]
   },
   {
@@ -346,12 +346,12 @@
      "data": {
       "text/plain": [
        "{'id': 'ga4gh:CN.WDzlT9oUq4IcQrVRWGH0dZnARnFBotCS',\n",
-       " 'type': 'CopyNumberCount',\n",
+       " 'type': <VrsType.CN_COUNT: 'CopyNumberCount'>,\n",
        " 'digest': 'WDzlT9oUq4IcQrVRWGH0dZnARnFBotCS',\n",
        " 'location': {'id': 'ga4gh:SL.H1Zh5xdBqamBjwVE9orWdY_uBkpEMH1V',\n",
-       "  'type': 'SequenceLocation',\n",
+       "  'type': <VrsType.SEQ_LOC: 'SequenceLocation'>,\n",
        "  'digest': 'H1Zh5xdBqamBjwVE9orWdY_uBkpEMH1V',\n",
-       "  'sequenceReference': {'type': 'SequenceReference',\n",
+       "  'sequenceReference': {'type': <VrsType.SEQ_REF: 'SequenceReference'>,\n",
        "   'refgetAccession': 'SQ.5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8'},\n",
        "  'start': 46111352,\n",
        "  'end': 46119948},\n",
@@ -364,8 +364,8 @@
     }
    ],
    "source": [
-    "allele = cnv_translator.translate_from(\"NC_000021.9:g.46111353_46119948del\", \"hgvs\", copies=\"1\")\n",
-    "allele.model_dump(exclude_none=True)"
+    "cnc = cnv_translator.translate_from(\"NC_000021.9:g.46111353_46119948del\", \"hgvs\", copies=\"1\")\n",
+    "cnc.model_dump(exclude_none=True)"
    ]
   }
  ],