Merge branch 'master' into HEAD

merge for new version
BojarLab · Dec 10, 2021 · 9798294 · 9798294
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Showing 70 changed files with 149,139 additions and 130,145 deletions.
diff --git a/00_core.ipynb b/00_core.ipynb
diff --git a/01_alignment.ipynb b/01_alignment.ipynb
@@ -1,5 +1,16 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "amazing-zambia",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#hide\n",
+    "#all_slow"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -18,6 +29,8 @@
    "source": [
     "#hide\n",
     "#default_exp alignment\n",
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")\n",
     "from nbdev.showdoc import show_doc\n",
     "from IPython.display import HTML\n",
     "%load_ext autoreload\n",
@@ -116,58 +129,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Test Alignment\n",
-      "1                                               9\n",
-      "Man a1-3 Man a1-4 Glc b1-4 Man a1-5 Kdo\n",
-      "Man a1-3 Man a1-3 Glc b1-6 Man a1-5 Kdo\n",
-      "Alignment Score: 21\n",
-      "Percent Identity: 77.77777777777779\n",
-      "Percent Coverage: 100.0\n",
-      "Sequence Index: GalA1P*a1-4*Man*a1-3*Man*a1-3*Glc*b1-6*Man*a1-5*Kdo\n",
-      "Species: []\n",
-      "\n",
-      "1                                               9\n",
-      "Man a1-3 Man a1-4 Glc b1-4 Man a1-5 Kdo\n",
-      "Man a1-3 Man a1-4 Glc b1-4 Man a1-5 Kdo\n",
-      "Alignment Score: 21\n",
-      "Percent Identity: 100.0\n",
-      "Percent Coverage: 100.0\n",
-      "Sequence Index: Man*a1-3*Man*a1-4*Glc*b1-4*Man*a1-5*Kdo\n",
-      "Species: ['Xanthomonas_oryzae']\n",
-      "\n",
-      "1                                                         9\n",
-      "Man a1-3 Man a1-4 Glc b1-4 Man -    -      a1-5 Kdo\n",
-      "Man a1-3 Man a1-3 Glc b1-6 Man a1-5 GalAOP a1-4 Kdo\n",
-      "Alignment Score: 19\n",
-      "Percent Identity: 54.54545454545454\n",
-      "Percent Coverage: 100.0\n",
-      "Sequence Index: Man*a1-3*Man*a1-3*Glc*b1-6*Man*a1-5*GalAOP*a1-4*Kdo\n",
-      "Species: ['Xanthomonas_campestris']\n",
-      "\n",
-      "1                                                         9\n",
-      "Man a1-3 Man a1-4 Glc -    -       b1-4 Man a1-5 Kdo\n",
-      "Man a1-3 Man a1-4 Glc b1-4 GalAOPN a1-3 Man a1-5 Kdo\n",
-      "Alignment Score: 19\n",
-      "Percent Identity: 72.72727272727273\n",
-      "Percent Coverage: 100.0\n",
-      "Sequence Index: Man*a1-3*Man*a1-4*Glc*b1-4*GalAOPN*a1-3*Man*a1-5*Kdo\n",
-      "Species: ['Xanthomonas_oryzae']\n",
-      "\n",
-      "1                                                         9\n",
-      "Man a1-3 Man a1-4 Glc b1-4 Man -    -    a1-5 Kdo\n",
-      "Man bond Man bond Glc bond Man bond GalA bond Kdo\n",
-      "Alignment Score: 19\n",
-      "Percent Identity: 45.45454545454545\n",
-      "Percent Coverage: 100.0\n",
-      "Sequence Index: Man*bond*Man*bond*Glc*bond*Man*bond*GalA*bond*Kdo\n",
-      "Species: []\n",
-      "\n"
+      "Test Alignment\n"
      ]
     }
    ],
    "source": [
     "print(\"Test Alignment\")\n",
-    "pairwiseAlign('Man(a1-3)Man(a1-4)Glc(b1-4)Man(a1-5)Kdo')\n",
+    "#pairwiseAlign('Man(a1-3)Man(a1-4)Glc(b1-4)Man(a1-5)Kdo')\n",
     "#pairwiseAlign('Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc')"
    ]
   },
@@ -196,6 +164,14 @@
     "#hide\n",
     "from nbdev.export import notebook2script; notebook2script()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fifty-train",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

diff --git a/02_glycan_data.ipynb b/02_glycan_data.ipynb
diff --git a/03_ml.ipynb b/03_ml.ipynb
diff --git a/04_motif.ipynb b/04_motif.ipynb
diff --git a/05_examples.ipynb b/05_examples.ipynb
diff --git a/06_network.ipynb b/06_network.ipynb
@@ -1,5 +1,16 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "established-winter",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#hide\n",
+    "#all_slow"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -9,6 +20,8 @@
    "source": [
     "#hide\n",
     "#default_exp network\n",
+    "import warnings\n",
+    "warnings.filterwarnings(\"ignore\")\n",
     "from nbdev.showdoc import show_doc\n",
     "from IPython.display import HTML\n",
     "%load_ext autoreload\n",
@@ -368,11 +381,11 @@
     {
      "data": {
       "text/plain": [
-       "([<networkx.classes.graph.Graph at 0x253994c4130>,\n",
-       "  <networkx.classes.graph.Graph at 0x253cd0cc640>,\n",
-       "  <networkx.classes.graph.Graph at 0x253cd0cc9d0>],\n",
-       " ['Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc',\n",
-       "  'Man(a1-3)Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc',\n",
+       "([<networkx.classes.graph.Graph at 0x1f231e922b0>,\n",
+       "  <networkx.classes.graph.Graph at 0x1f231e923a0>,\n",
+       "  <networkx.classes.graph.Graph at 0x1f231e92160>],\n",
+       " ['Man(a1-3)Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc',\n",
+       "  'Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc',\n",
        "  'Man(a1-6)Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc'])"
       ]
      },