From 4c524676cd0851b2bfe67a4ed5b02ea5f880652f Mon Sep 17 00:00:00 2001
From: Sean Upchurch <sau@alumni.caltech.edu>
Date: Fri, 17 Feb 2017 10:33:33 -0800
Subject: [PATCH] remove feature_id search on ExpressionLevel

---
 python_notebooks/1kg_rna_analysis_example.ipynb | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/python_notebooks/1kg_rna_analysis_example.ipynb b/python_notebooks/1kg_rna_analysis_example.ipynb
index 9b6f0a0..6469477 100644
--- a/python_notebooks/1kg_rna_analysis_example.ipynb
+++ b/python_notebooks/1kg_rna_analysis_example.ipynb
@@ -136,11 +136,9 @@
     "    if counter > 5:\n",
     "        break\n",
     "    counter += 1\n",
-    "    if expression.feature_id != \"\":\n",
-    "        expression_levels.append(expression)\n",
+    "    expression_levels.append(expression)\n",
     "    print(\"Expression Level: {}\".format(expression.name))\n",
     "    print(\" id: {}\".format(expression.id))\n",
-    "    print(\" feature: {}\".format(expression.feature_id))\n",
     "    print(\" expression: {} {}\".format(expression.expression, getUnits(expression.units)))\n",
     "    print(\" read_count: {}\".format(expression.raw_read_count))\n",
     "    print(\" confidence_interval: {} - {}\\n\".format(\n",
@@ -154,7 +152,7 @@
    },
    "source": [
     "### Finding Features in the other RNA Quantifications\n",
-    "We can also easily examine the expression level of these features in the other RNA Quantifications by specifying the feature_id in the `expressionLevelSearch`."
+    "We can also easily examine the expression level of these features in the other RNA Quantifications by specifying the name in the `expressionLevelSearch`."
    ]
   },
   {
@@ -165,14 +163,13 @@
    },
    "outputs": [],
    "source": [
-    "feature_ids = [expression_levels[1].feature_id]\n",
+    "names = [expression_levels[1].name]\n",
     "for rna_quantification_id in rna_quantification_ids[1:]:\n",
     "    for expression in local_client.search_expression_levels(\n",
-    "            rna_quantification_id=rna_quantification_id, feature_ids=feature_ids):\n",
+    "            rna_quantification_id=rna_quantification_id, names=names):\n",
     "        print(\"RNA Quantification: {}\".format(rna_quantification_id))\n",
     "        print(\"Expression Level: {}\".format(expression.name))\n",
     "        print(\" id: {}\".format(expression.id))\n",
-    "        print(\" feature: {}\".format(expression.feature_id))\n",
     "        print(\" expression: {} {}\\n\".format(expression.expression, getUnits(expression.units)))\n"
    ]
   },
@@ -202,8 +199,7 @@
     "        if counter > max_features:\n",
     "            break\n",
     "        counter += 1\n",
-    "        if expression.feature_id != \"\":\n",
-    "            expression_dict[expression.name] = expression.expression\n",
+    "        expression_dict[expression.name] = expression.expression\n",
     "    return expression_dict\n",
     "\n",
     "\n",
@@ -275,7 +271,7 @@
     "        if counter > max_features:\n",
     "            break\n",
     "        counter += 1\n",
-    "        if expression.feature_id != \"\" and expression.raw_read_count > 0:\n",
+    "        if expression.raw_read_count > 0:\n",
     "            expression_dict[expression.name] = expression.raw_read_count\n",
     "    return quantification.name, expression_dict\n",
     "\n",