Update B2B_Tools_MSA_Example_In_function_of_a_protein's_behavior.ipynb

Update to version b2btools v3.0.8b3

Author: agdiaz

B2B_Tools_MSA_Example_In_function_of_a_protein's_behavior.ipynb

@@ -53,66 +53,12 @@
  "id": "-BBDAd3jwjDd"
  }
  },
- {
- "cell_type": "markdown",
- "source": [
- "# 1.a Install the Pomegranate Package"
- ],
- "metadata": {
- "id": "KAHMTKzMfvMc"
- }
- },
- {
- "cell_type": "code",
- "source": [
- "\n",
- "#@title First step : install the cython and scipy dependencies\n",
- "%%capture\n",
- "!pip install \"cython~=0.29.14\" \"scipy>=0.17.0\""
- ],
- "metadata": {
- "cellView": "form",
- "id": "FaTJZBwucDyu"
- },
- "execution_count": 1,
- "outputs": []
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {
- "cellView": "form",
- "id": "FpnQ_Uwsa0vE"
- },
- "outputs": [],
- "source": [
- "#@title Second step : Search the pomegranate package on Github\n",
- "%%capture\n",
- "!git clone -b v0.14.9 --single-branch https://github.com/jmschrei/pomegranate.git"
- ]
- },
- {
- "cell_type": "code",
- "source": [
- "#@title Last step : Install the pomegranate package\n",
- "%%capture\n",
- "#@markdown Please be patient, this can take several minutes...\n",
- "%cd pomegranate\n",
- "!python setup.py install"
- ],
- "metadata": {
- "cellView": "form",
- "id": "U7PAH0hxa_cx"
- },
- "execution_count": 3,
- "outputs": []
- },
  {
  "cell_type": "code",
  "source": [
- "#@title 1.b Install the B2BTools Package\n",
+ "#@title 1.a Install the B2BTools Package\n",
  "%%capture\n",
- "!pip install b2bTools==3.0.7 ipympl hmmer\n",
+ "!pip install b2bTools==3.0.8b3 ipympl hmmer\n",
  "#@markdown Please be patient, this can take several minutes...\n",
  "\n",
  "#@markdown ⚠️ Once installed, please restart the session and run step 1.c directly, without rerunning the first step."
@@ -121,13 +67,13 @@
  "cellView": "form",
  "id": "Pay97KNHiL_E"
  },
- "execution_count": 4,
+ "execution_count": null,
  "outputs": []
  },
  {
  "cell_type": "code",
  "source": [
- "#@title 1.c Install the dependencies\n",
+ "#@title 1.b Install the dependencies\n",
  "%%capture\n",
  "import math\n",
  "import Bio\n",
@@ -147,13 +93,13 @@
  "cellView": "form",
  "id": "LuFTJyt2jE49"
  },
- "execution_count": 1,
+ "execution_count": null,
  "outputs": []
  },
  {
  "cell_type": "code",
  "source": [
- "#@title 1.d Upload your MSA file\n",
+ "#@title 1.c Upload your MSA file\n",
  "\n",
  "#@markdown Execute this cell to upload your MSA file from your computer.\n",
  "\n",
@@ -278,7 +224,7 @@
  "cellView": "form",
  "id": "jVbBi3NHj_L8"
  },
- "execution_count": 3,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -367,7 +313,7 @@
  "cellView": "form",
  "id": "13vD_D2rmxWj"
  },
- "execution_count": 5,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -457,7 +403,7 @@
  "cellView": "form",
  "id": "Ko2mHtQWm7CW"
  },
- "execution_count": 6,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -612,7 +558,7 @@
  "cellView": "form",
  "id": "iVXazSQInABW"
  },
- "execution_count": 7,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -728,7 +674,7 @@
  "cellView": "form",
  "id": "68uRbfpMnFpy"
  },
- "execution_count": 8,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -895,7 +841,7 @@
  "cellView": "form",
  "id": "rRdPAR0snMdz"
  },
- "execution_count": 9,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -1057,7 +1003,7 @@
  "cellView": "form",
  "id": "80hzPgLSnVcv"
  },
- "execution_count": 10,
+ "execution_count": null,
  "outputs": []
  },
  {
@@ -1247,14 +1193,13 @@
  "cellView": "form",
  "id": "60AQ3g96negH"
  },
- "execution_count": 11,
+ "execution_count": null,
  "outputs": []
  },
  {
  "cell_type": "code",
  "source": [
  "#@title 6. Get the Gaussian Mixture Model (GMM) scores\n",
- "%%capture\n",
  "#@markdown Once this cell has been executed, the GMM scores will be computed and the most different residues will be shown.\n",
  "#@markdown The results are also saved in the Results folder.\n",
  "\n",
@@ -1319,8 +1264,9 @@
  "\n",
  " # Ensure 'predictions_single_seq' exists and is correctly defined\n",
  " if 'predictions_single_seq' in globals():\n",
- " for prot in predictions_single_seq[\"sequence\"].keys():\n",
- " sequences[prot] = predictions_single_seq[\"sequence\"][prot]\n",
+ " for prot_index, prot in enumerate(predictions_single_seq.keys()):\n",
+ " assert prot == msaSuite.seqs[prot_index][0]\n",
+ " sequences[prot] = msaSuite.seqs[prot_index][1]\n",
  " else:\n",
  " raise KeyError(\"predictions_single_seq not found in the global scope\")\n",
  "\n",
@@ -1409,7 +1355,7 @@
  "cellView": "form",
  "id": "eOq1COBVnjkA"
  },
- "execution_count": 12,
+ "execution_count": null,
  "outputs": []
  },
  {