diff --git a/corneto/methods/metabolism/__init__.py b/corneto/methods/metabolism/__init__.py index 1c2f6c0..d2b90d3 100644 --- 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 index 6271da8..e55b7d2 100644 --- 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",