Export metabolism util methods to clean up notebooks

saezlab · May 8, 2024 · 8f50d0b · 8f50d0b
1 parent 4ac6c63
commit 8f50d0b
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Showing 2 changed files with 15 additions and 6 deletions.
diff --git a/corneto/methods/metabolism/__init__.py b/corneto/methods/metabolism/__init__.py
@@ -1 +1,13 @@
-from corneto.methods.metabolism._utils import evaluate_gpr_rules
+from corneto.methods.metabolism._utils import (
+    evaluate_gpr_expression,
+    evaluate_gpr_rules,
+    get_genes_from_gpr,
+    get_unique_genes,
+)
+
+__all__ = [
+    "evaluate_gpr_rules",
+    "get_unique_genes",
+    "get_genes_from_gpr",
+    "evaluate_gpr_expression",
+]
diff --git a/docs/tutorials/context-specific-metabolic-omics.ipynb b/docs/tutorials/context-specific-metabolic-omics.ipynb
@@ -38,6 +38,7 @@
     }
    ],
    "source": [
+    "import numpy as np\n",
     "import pandas as pd\n",
     "\n",
     "import corneto as cn\n",
@@ -560,7 +561,7 @@
     }
    ],
    "source": [
-    "from corneto.methods.metabolism._utils import get_unique_genes\n",
+    "from corneto.methods.metabolism import evaluate_gpr_expression, get_unique_genes\n",
     "\n",
     "genes = get_unique_genes(G, startswith=\"b\")\n",
     "len(genes)"
@@ -819,8 +820,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from corneto.methods.metabolism._utils import evaluate_gpr_expression\n",
-    "\n",
     "values = df_expr[[\"gene\", \"score\"]].set_index(\"gene\").to_dict()[\"score\"]\n",
     "e = evaluate_gpr_expression(G.get_attr_from_edges(\"GPR\"), values)"
    ]
@@ -842,8 +841,6 @@
     }
    ],
    "source": [
-    "import numpy as np\n",
-    "\n",
     "from corneto.methods.metabolism.fba import multicondition_imat\n",
     "\n",
     "P = multicondition_imat(G, np.array(e))\n",