try seq_alignment pypi package.ipynb

try-seq_alignment-pypi-package.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "try  seq_alignment pypi package.ipynb",
      "provenance": [],
      "collapsed_sections": [],
      "authorship_tag": "ABX9TyPowmeLcCUpdHQn3t4cyKQJ",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/gist/shadiakiki1986/cb35201984f4bf3c0678652a6aeb580d/try-seq_alignment-pypi-package.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "w2_k_Yjp3EzD"
      },
      "source": [
        "Example usage of https://github.com/ryanlstevens/seq_alignment"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "dchgdzjM267p"
      },
      "source": [
        "!pip install --quiet seq_alignment"
      ],
      "execution_count": 1,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "xowItfL_3Hdu"
      },
      "source": [
        "# fro readme\n",
        "from seq_alignment import global_similarity\n",
        "\n",
        "# Test values\n",
        "str1=list(\"vina one\")\n",
        "str2=list(\"vin yard one\")\n",
        "\n",
        "# Initalize matching class function\n",
        "sim_init = global_similarity(str1,str2,backtrace=True) # False\n",
        "\n",
        "# Run matching \n",
        "sim_init.run()"
      ],
      "execution_count": 5,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "9Zfie0DJ3LwB",
        "outputId": "2bbbf531-d3b3-485b-d515-8070c0316d58"
      },
      "source": [
        "# Get edit distance\n",
        "print(\"EDIT DISTANCE\")\n",
        "print(sim_init.match_distance)"
      ],
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "EDIT DISTANCE\n",
            "-4\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "jZ1jjt9E3SB2",
        "outputId": "21903b55-e66d-4783-d70a-d0967cdf61cf"
      },
      "source": [
        "print(\"\\n\".join([\"\".join(x) for x in sim_init.match_alignment_table]))"
      ],
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "vin  a   one\n",
            "vin yard one\n",
            "SSSIISIISSSS\n"
          ]
        }
      ]
    }
  ]
}