From b5f093b4b7f3366c3c123a7c88df201e835802cd Mon Sep 17 00:00:00 2001
From: Sumner <mag.ds@live.com>
Date: Wed, 23 Oct 2019 18:39:21 +0200
Subject: [PATCH] added encode to notebook

---
 jupyter/LabeledRanges.ipynb | 707 ++++++++++++++----------------------
 1 file changed, 272 insertions(+), 435 deletions(-)

diff --git a/jupyter/LabeledRanges.ipynb b/jupyter/LabeledRanges.ipynb
index 7082b55..3f230ab 100644
--- a/jupyter/LabeledRanges.ipynb
+++ b/jupyter/LabeledRanges.ipynb
@@ -2,36 +2,37 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
     "from ntai import Labeler\n",
     "# from ntai.ranges.labeled_ranges import LabeledRange, LabeledRanges\n",
-    "from lrng import LabeledRange, LabeledRanges"
+    "from lrng import LabeledRange, LabeledRanges\n",
+    "import numpy as np"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
-    "l = Labeler(label_order=['b', 'a'], processes=10)"
+    "l = Labeler(label_order=['b', 'a'], processes=10, use_other_class=False)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "<ntai.labeler.labeler.Labeler at 0x7fbc3034d668>"
+       "<ntai.labeler.labeler.Labeler at 0x124ff7d50>"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -42,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -51,215 +52,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
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-       "       [0, 0, 1],\n",
-       "       [0, 0, 1],\n",
-       "       [0, 0, 1],\n",
-       "       [0, 0, 1]])"
+       "array([[0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1],\n",
+       "       [0, 1]])"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -267,269 +78,295 @@
    "source": [
     "seq=[i for i in range(300-100)]\n",
     "enc = l.encode(seq, crngs, 100)\n",
-    "enc"
+    "np.array(enc)[:10]"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
      "data": {
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-       " [0, 0, 1],\n",
-       " [0, 0, 1]]"
+       "LabeledRanges(\n",
+       "\tLabeledRange('b', 150, 250)\n",
+       "\tLabeledRange('a', 100, 200)\n",
+       ")"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "enc.tolist()"
+    "rel = l.label(\n",
+    "    [\n",
+    "        'chr1', 100, 300, 'name', '0', '-'\n",
+    "    ],\n",
+    "    {\n",
+    "        'chr1': {\n",
+    "            '-': LabeledRanges([\n",
+    "                ['a', 100, 200], ['b',150,250],\n",
+    "                ['a', 10, 20], ['b',15,25]\n",
+    "            ])\n",
+    "        }\n",
+    "    }\n",
+    ")\n",
+    "rel"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "LabeledRanges(\n",
-       "\tLabeledRange('a', 100, 200)\n",
-       "\tLabeledRange('b', 150, 250)\n",
-       ")"
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+       " [0, 1],\n",
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+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 1],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
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+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [1, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0],\n",
+       " [0, 0]]"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 21,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "l.label(\n",
+    "l.encode(\n",
+    "    'a'*200, \n",
+    "#     rel, \n",
     "    [\n",
-    "        'chr1', 100, 300, 'name', '0', '-'\n",
-    "    ],\n",
-    "    {\n",
-    "        'chr1': {\n",
-    "            '-': LabeledRanges([\n",
-    "                ['a', 100, 200], ['b',150,250],\n",
-    "                ['a', 10, 20], ['b',15,25]\n",
-    "            ])\n",
-    "        }\n",
-    "    }\n",
+    "        ['a', 100, 200],\n",
+    "        ['b', 150, 250],\n",
+    "#         ['c', 100, 200],\n",
+    "    ],    \n",
+    "    100\n",
     ")"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "LabeledRanges(\n",
+       "\tLabeledRange('b', 150, 250)\n",
+       "\tLabeledRange('a', 100, 200)\n",
+       ")"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rel + ['c', 100, 200]"
+   ]
   },
   {
    "cell_type": "code",
@@ -555,7 +392,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.8"
+   "version": "3.7.4"
   },
   "toc": {
    "base_numbering": 1,
-- 
GitLab