notebooks/Plotting_ribotricer_profile.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "provenance": [],
      "collapsed_sections": [],
      "authorship_tag": "ABX9TyNmFOPf4woqMkk+kE/xrrH4",
      "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/github/smithlabcode/ribotricer/blob/master/notebooks/Plotting_ribotricer_profile.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "LhyXCSwqc6Ds",
        "outputId": "f3c9da6d-5694-4a3e-e0f2-318b82d4bf77"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n",
            "Collecting git+https://github.com/smithlabcode/ribotricer\n",
            "  Cloning https://github.com/smithlabcode/ribotricer to /tmp/pip-req-build-hzb1gxqa\n",
            "  Running command git clone -q https://github.com/smithlabcode/ribotricer /tmp/pip-req-build-hzb1gxqa\n",
            "Requirement already satisfied: click>=8.1.3 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (8.1.3)\n",
            "Requirement already satisfied: click-help-colors>=0.9.1 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (0.9.1)\n",
            "Requirement already satisfied: matplotlib>=3.5.3 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (3.5.3)\n",
            "Requirement already satisfied: numpy>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (1.21.6)\n",
            "Requirement already satisfied: pandas>=1.3 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (1.3.5)\n",
            "Requirement already satisfied: pyfaidx>=0.7.1 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (0.7.1)\n",
            "Requirement already satisfied: pysam>=0.19.1 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (0.19.1)\n",
            "Requirement already satisfied: quicksect>=0.2.2 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (0.2.2)\n",
            "Requirement already satisfied: scipy>=1.7.0 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (1.7.3)\n",
            "Requirement already satisfied: tqdm>=4.64.1 in /usr/local/lib/python3.7/dist-packages (from ribotricer==1.3.2) (4.64.1)\n",
            "Requirement already satisfied: importlib-metadata in /usr/local/lib/python3.7/dist-packages (from click>=8.1.3->ribotricer==1.3.2) (4.12.0)\n",
            "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (2.8.2)\n",
            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (1.4.4)\n",
            "Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (7.1.2)\n",
            "Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (4.37.3)\n",
            "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (21.3)\n",
            "Requirement already satisfied: pyparsing>=2.2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (3.0.9)\n",
            "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=3.5.3->ribotricer==1.3.2) (0.11.0)\n",
            "Requirement already satisfied: typing-extensions in /usr/local/lib/python3.7/dist-packages (from kiwisolver>=1.0.1->matplotlib>=3.5.3->ribotricer==1.3.2) (4.1.1)\n",
            "Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.3->ribotricer==1.3.2) (2022.2.1)\n",
            "Requirement already satisfied: setuptools>=0.7 in /usr/local/lib/python3.7/dist-packages (from pyfaidx>=0.7.1->ribotricer==1.3.2) (57.4.0)\n",
            "Requirement already satisfied: six in /usr/local/lib/python3.7/dist-packages (from pyfaidx>=0.7.1->ribotricer==1.3.2) (1.15.0)\n",
            "Requirement already satisfied: cython in /usr/local/lib/python3.7/dist-packages (from quicksect>=0.2.2->ribotricer==1.3.2) (0.29.32)\n",
            "Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.7/dist-packages (from importlib-metadata->click>=8.1.3->ribotricer==1.3.2) (3.8.1)\n"
          ]
        }
      ],
      "source": [
        "pip install git+https://github.com/smithlabcode/ribotricer"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget -c https://www.dropbox.com/s/xr0xsdluuni2b95/ribotricer_test_data_tair10.zip"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "m9_tjevedgTL",
        "outputId": "3865dce9-9c7f-4679-ee5d-4177c6e693c5"
      },
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2022-09-28 20:53:11--  https://www.dropbox.com/s/xr0xsdluuni2b95/ribotricer_test_data_tair10.zip\n",
            "Resolving www.dropbox.com (www.dropbox.com)... 162.125.6.18, 2620:100:601c:18::a27d:612\n",
            "Connecting to www.dropbox.com (www.dropbox.com)|162.125.6.18|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: /s/raw/xr0xsdluuni2b95/ribotricer_test_data_tair10.zip [following]\n",
            "--2022-09-28 20:53:11--  https://www.dropbox.com/s/raw/xr0xsdluuni2b95/ribotricer_test_data_tair10.zip\n",
            "Reusing existing connection to www.dropbox.com:443.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: https://ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com/cd/0/inline/Bt0gWivkcupzujjGEP1XNgtwjnUDusLkl5ZtQ2ScfDbp7L3pehZFEzowwE6LgVVI3KM3w6wtc85OVM7yUmGJ-Pqv0VnkrwyEHjoYJhz25wPNLW5P_NsXvkSHj4yAcg5yCJwgi8Prv7L__ShZjcvS_gtgo4DIYUE4BVXpIwUMRyZqBg/file# [following]\n",
            "--2022-09-28 20:53:11--  https://ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com/cd/0/inline/Bt0gWivkcupzujjGEP1XNgtwjnUDusLkl5ZtQ2ScfDbp7L3pehZFEzowwE6LgVVI3KM3w6wtc85OVM7yUmGJ-Pqv0VnkrwyEHjoYJhz25wPNLW5P_NsXvkSHj4yAcg5yCJwgi8Prv7L__ShZjcvS_gtgo4DIYUE4BVXpIwUMRyZqBg/file\n",
            "Resolving ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com (ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com)... 162.125.4.15, 2620:100:601c:15::a27d:60f\n",
            "Connecting to ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com (ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com)|162.125.4.15|:443... connected.\n",
            "HTTP request sent, awaiting response... 302 Found\n",
            "Location: /cd/0/inline2/Bt2Ur9RcQZBDrcUEBBnM9UtbL47xwjLc281mTaXBC-RfF6kHbY4PenQtRBC_nC_2oqeY6f5rlt_tnEuqxCXml6StXsCf7QiFiUauapO9Sm0q1TBMZjjrZz6s9suL4PH814KIM2fKBUecdCVZXcSvagB42t_A0WILCKHFmePCmZxu45ci1GAQPDbcpqpazWhNPEPgkHt4mlUdh0lDZaiW1gKrEO9FQNXsdtj78WO0Ik69-JwzCU6Y7zCZxvfySeNyOerzhoUBIJxuK_xb5et-zzYefMZ2yNyesAniXcZPOhx39tQqf3lzsrJ_BD-FzC_Z-eroFOfKTzb20fLqu491qt36-CvoIfn7TF_AHPjFVKgKK16iqdmZoWk55fViEgXkYXAySV8MhZbnI2qRCyHFalbBp74gkKMq6SghXKyNIF091Q/file [following]\n",
            "--2022-09-28 20:53:11--  https://ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com/cd/0/inline2/Bt2Ur9RcQZBDrcUEBBnM9UtbL47xwjLc281mTaXBC-RfF6kHbY4PenQtRBC_nC_2oqeY6f5rlt_tnEuqxCXml6StXsCf7QiFiUauapO9Sm0q1TBMZjjrZz6s9suL4PH814KIM2fKBUecdCVZXcSvagB42t_A0WILCKHFmePCmZxu45ci1GAQPDbcpqpazWhNPEPgkHt4mlUdh0lDZaiW1gKrEO9FQNXsdtj78WO0Ik69-JwzCU6Y7zCZxvfySeNyOerzhoUBIJxuK_xb5et-zzYefMZ2yNyesAniXcZPOhx39tQqf3lzsrJ_BD-FzC_Z-eroFOfKTzb20fLqu491qt36-CvoIfn7TF_AHPjFVKgKK16iqdmZoWk55fViEgXkYXAySV8MhZbnI2qRCyHFalbBp74gkKMq6SghXKyNIF091Q/file\n",
            "Reusing existing connection to ucfbf0093834dbed7b6d128ed399.dl.dropboxusercontent.com:443.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "\n",
            "    The file is already fully retrieved; nothing to do.\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!unzip ribotricer_test_data_tair10.zip"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "tgYfYEacdoze",
        "outputId": "276a3310-d2ed-4d16-88f5-d76a4f5da65b"
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Archive:  ribotricer_test_data_tair10.zip\n",
            "replace ribotricer_test_data_tair10/bams_unique/SRX219170.bam? [y]es, [n]o, [A]ll, [N]one, [r]ename: N\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "from collections import Counter\n",
        "from itertools import cycle\n",
        "from itertools import islice\n",
        "import os\n",
        "import sys\n",
        "import six\n",
        "import matplotlib.pyplot as plt\n",
        "from matplotlib.ticker import MultipleLocator\n",
        "from matplotlib.ticker import FormatStrFormatter\n",
        "from matplotlib.ticker import LinearLocator\n",
        "from matplotlib.ticker import MaxNLocator\n",
        "from matplotlib.ticker import AutoMinorLocator\n",
        "__FRAME_COLORS__ = [\"#fc8d62\", \"#66c2a5\", \"#8da0cb\"]\n",
        "\n",
        "def set_xrotation(ax, degrees):\n",
        "    \"\"\"Rotate labels on x-axis.\n",
        "    Parameters\n",
        "    ----------\n",
        "    ax : matplotlib.Axes\n",
        "         Axes object\n",
        "    degrees : int\n",
        "              Rotation degrees\n",
        "    \"\"\"\n",
        "    for i in ax.get_xticklabels():\n",
        "        i.set_rotation(degrees)\n",
        "\n",
        "\n",
        "def millify(n):\n",
        "    \"\"\"Convert integer to human readable format.\n",
        "    Parameters\n",
        "    ----------\n",
        "    n : int\n",
        "    Returns\n",
        "    -------\n",
        "    millidx : str\n",
        "              Formatted integer\n",
        "    \"\"\"\n",
        "    if n is None or np.isnan(n):\n",
        "        return \"NaN\"\n",
        "    millnames = [\"\", \" K\", \" M\", \" B\", \" T\"]\n",
        "    # Source: http://stackoverflow.com/a/3155023/756986\n",
        "    n = float(n)\n",
        "    millidx = max(\n",
        "        0,\n",
        "        min(\n",
        "            len(millnames) - 1, int(math.floor(0 if n == 0 else math.log10(abs(n)) / 3))\n",
        "        ),\n",
        "    )\n",
        "\n",
        "    return \"{:.1f}{}\".format(n / 10 ** (3 * millidx), millnames[millidx])\n",
        "\n",
        "\n",
        "\n",
        "def setup_axis(ax, axis=\"x\", majorticks=5, minorticks=1, xrotation=45, yrotation=0):\n",
        "    \"\"\"Setup axes defaults\n",
        "    Parameters\n",
        "    ----------\n",
        "    ax : matplotlib.Axes\n",
        "    axis : str\n",
        "           Setup 'x' or 'y' axis\n",
        "    majorticks : int\n",
        "                 Length of interval between two major ticks\n",
        "    minorticks : int\n",
        "                 Length of interval between two major ticks\n",
        "    xrotation : int\n",
        "                Rotate x axis labels by xrotation degrees\n",
        "    yrotation : int\n",
        "                Rotate x axis labels by xrotation degrees\n",
        "    \"\"\"\n",
        "    major_locator = MultipleLocator(majorticks)\n",
        "    major_formatter = FormatStrFormatter(\"%d\")\n",
        "    minor_locator = MultipleLocator(minorticks)\n",
        "    if axis == \"x\":\n",
        "        ax.xaxis.set_major_locator(major_locator)\n",
        "        ax.xaxis.set_major_formatter(major_formatter)\n",
        "        ax.xaxis.set_minor_locator(minor_locator)\n",
        "    elif axis == \"y\":\n",
        "        ax.yaxis.set_major_locator(major_locator)\n",
        "        ax.yaxis.set_major_formatter(major_formatter)\n",
        "        ax.yaxis.set_minor_locator(minor_locator)\n",
        "    elif axis == \"both\":\n",
        "        setup_axis(ax, \"x\", majorticks, minorticks, xrotation, yrotation)\n",
        "        setup_axis(ax, \"y\", majorticks, minorticks, xrotation, yrotation)\n",
        "    ax.yaxis.set_major_locator(MaxNLocator(integer=True))\n",
        "    ax.tick_params(which=\"major\", width=2, length=10)\n",
        "    ax.tick_params(which=\"minor\", width=1, length=6)\n",
        "    ax.tick_params(axis=\"x\", labelrotation=xrotation)\n",
        "    ax.tick_params(axis=\"y\", labelrotation=yrotation)\n",
        "\n",
        "\n",
        "\n",
        "def plot_framewise_counts(\n",
        "    counts,\n",
        "    frames_to_plot=\"all\",\n",
        "    ax=None,\n",
        "    title=None,\n",
        "    millify_labels=False,\n",
        "    position_range=None,\n",
        "    saveto=None,\n",
        "    **kwargs\n",
        "):\n",
        "    \"\"\"Plot framewise distribution of reads.\n",
        "    Parameters\n",
        "    ----------\n",
        "    counts : Series\n",
        "             A series with position as index and value as counts\n",
        "    frames_to_plot : str or range\n",
        "                     A comma seaprated list of frames to highlight or a range\n",
        "    ax : matplotlib.Axes\n",
        "         Default none\n",
        "    saveto : str\n",
        "             Path to save output file to (<filename>.png/<filename>.pdf)\n",
        "    \"\"\"\n",
        "    \n",
        "    if isinstance(counts, Counter):\n",
        "        counts = pd.Series(counts)\n",
        "    if isinstance(frames_to_plot, six.string_types) and frames_to_plot != \"all\":\n",
        "        frames_to_plot = list([int(x) for x in frames_to_plot.rstrip().split(\",\")])\n",
        "    if isinstance(position_range, six.string_types):\n",
        "        splitted = list([int(x) for x in position_range.strip().split(\":\")])\n",
        "        position_range = list(range(splitted[0], splitted[1] + 1))\n",
        "\n",
        "    if position_range:\n",
        "        counts = counts[list(position_range)]\n",
        "    fig = None\n",
        "    if ax is None:\n",
        "        fig, ax = plt.subplots()\n",
        "    else:\n",
        "        fig = ax.get_figure()\n",
        "    if \"majorticks\" not in kwargs:\n",
        "        kwargs[\"majorticks\"] = 10\n",
        "    if \"minorticks\" not in kwargs:\n",
        "        kwargs[\"minorticks\"] = 5\n",
        "    if \"xrotation\" not in kwargs:\n",
        "        kwargs[\"xrotation\"] = 90\n",
        "\n",
        "    setup_axis(ax, **kwargs)\n",
        "    ax.set_ylabel(\"Number of reads\")\n",
        "\n",
        "    barlist = ax.bar(counts.index, counts.values)\n",
        "    barplot_colors = list(islice(cycle(__FRAME_COLORS__), None, len(counts.index)))\n",
        "    for index, cbar in enumerate(barlist):\n",
        "        cbar.set_color(barplot_colors[index])\n",
        "    ax.legend(\n",
        "        (barlist[0], barlist[1], barlist[2]),\n",
        "        (\"Frame 1\", \"Frame 2\", \"Frame 3\"),\n",
        "        bbox_to_anchor=(0.0, 1.02, 1.0, 0.102),\n",
        "        loc=3,\n",
        "        ncol=3,\n",
        "        mode=\"expand\",\n",
        "        borderaxespad=0.0,\n",
        "    )\n",
        "    if title:\n",
        "        ax.set_title(title)\n",
        "    if millify_labels:\n",
        "        ax.set_yticklabels(list([millify(x) for x in ax.get_yticks()]))\n",
        "    \n",
        "    set_xrotation(ax, kwargs[\"xrotation\"])\n",
        "    fig.tight_layout()\n",
        "    if saveto:\n",
        "        fig.tight_layout()\n",
        "        fig.savefig(saveto, dpi=DPI)\n",
        "    return ax"
      ],
      "metadata": {
        "id": "65K-qDN6dv_s"
      },
      "execution_count": 5,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "# read results from one of the frames\n",
        "import pandas as pd\n",
        "ribotricer_df = pd.read_csv(\"ribotricer_test_data_tair10/translating_ORFs/SRX219170_translating_ORFs.tsv\", sep=\"\\t\").set_index(\"ORF_ID\")\n",
        "ribotricer_df = ribotricer_df.sort_values(by='valid_codons_ratio', ascending=False)\n",
        "ribotricer_df.head()"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 649
        },
        "id": "zz8s6tH6ehrz",
        "outputId": "fad7a7dd-2c94-4a84-8635-6cfd2f8129f8"
      },
      "execution_count": 6,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "                                    ORF_type       status  phase_score  \\\n",
              "ORF_ID                                                                   \n",
              "AT4G15610.2_8909332_8909406_75          uORF  translating     0.855545   \n",
              "AT1G68530.2_25712993_25713052_60        dORF  translating     0.819610   \n",
              "AT5G48485.1_19646320_19646625_306  annotated  translating     0.803626   \n",
              "AT1G60950.1_22444565_22445008_444  annotated  translating     0.861726   \n",
              "AT1G62660.2_23200187_23200300_114       uORF  translating     0.821548   \n",
              "\n",
              "                                   read_count  length  valid_codons  \\\n",
              "ORF_ID                                                                \n",
              "AT4G15610.2_8909332_8909406_75            746      75            25   \n",
              "AT1G68530.2_25712993_25713052_60          199      60            20   \n",
              "AT5G48485.1_19646320_19646625_306        2094     306           102   \n",
              "AT1G60950.1_22444565_22445008_444        7208     444           148   \n",
              "AT1G62660.2_23200187_23200300_114         589     114            38   \n",
              "\n",
              "                                   valid_codons_ratio  read_density  \\\n",
              "ORF_ID                                                                \n",
              "AT4G15610.2_8909332_8909406_75                    1.0     29.840000   \n",
              "AT1G68530.2_25712993_25713052_60                  1.0      9.950000   \n",
              "AT5G48485.1_19646320_19646625_306                 1.0     20.529412   \n",
              "AT1G60950.1_22444565_22445008_444                 1.0     48.702703   \n",
              "AT1G62660.2_23200187_23200300_114                 1.0     15.500000   \n",
              "\n",
              "                                  transcript_id transcript_type    gene_id  \\\n",
              "ORF_ID                                                                       \n",
              "AT4G15610.2_8909332_8909406_75      AT4G15610.2  protein_coding  AT4G15610   \n",
              "AT1G68530.2_25712993_25713052_60    AT1G68530.2  protein_coding  AT1G68530   \n",
              "AT5G48485.1_19646320_19646625_306   AT5G48485.1  protein_coding  AT5G48485   \n",
              "AT1G60950.1_22444565_22445008_444   AT1G60950.1  protein_coding  AT1G60950   \n",
              "AT1G62660.2_23200187_23200300_114   AT1G62660.2  protein_coding  AT1G62660   \n",
              "\n",
              "                                   gene_name       gene_type chrom strand  \\\n",
              "ORF_ID                                                                      \n",
              "AT4G15610.2_8909332_8909406_75     AT4G15610  protein_coding     4      +   \n",
              "AT1G68530.2_25712993_25713052_60        CUT1  protein_coding     1      -   \n",
              "AT5G48485.1_19646320_19646625_306       DIR1  protein_coding     5      -   \n",
              "AT1G60950.1_22444565_22445008_444        FD2  protein_coding     1      +   \n",
              "AT1G62660.2_23200187_23200300_114    BFRUCT3  protein_coding     1      +   \n",
              "\n",
              "                                  start_codon  \\\n",
              "ORF_ID                                          \n",
              "AT4G15610.2_8909332_8909406_75            ATT   \n",
              "AT1G68530.2_25712993_25713052_60          AGG   \n",
              "AT5G48485.1_19646320_19646625_306         ATG   \n",
              "AT1G60950.1_22444565_22445008_444         ATG   \n",
              "AT1G62660.2_23200187_23200300_114         ACG   \n",
              "\n",
              "                                                                             profile  \n",
              "ORF_ID                                                                                \n",
              "AT4G15610.2_8909332_8909406_75     [17, 2, 4, 21, 3, 2, 11, 12, 0, 16, 3, 1, 8, 4...  \n",
              "AT1G68530.2_25712993_25713052_60   [12, 3, 1, 10, 1, 1, 5, 7, 1, 6, 1, 2, 3, 0, 4...  \n",
              "AT5G48485.1_19646320_19646625_306  [9, 0, 4, 0, 0, 1, 1, 1, 4, 6, 5, 6, 0, 0, 1, ...  \n",
              "AT1G60950.1_22444565_22445008_444  [55, 2, 9, 6, 3, 11, 4, 4, 33, 3, 7, 26, 5, 3,...  \n",
              "AT1G62660.2_23200187_23200300_114  [2, 7, 2, 1, 10, 0, 0, 30, 3, 1, 15, 2, 1, 14,...  "
            ],
            "text/html": [
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              "  <div id=\"df-6c59fcdb-895a-440a-b568-e3d766e1ac29\">\n",
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              "    <tr style=\"text-align: right;\">\n",
              "      <th></th>\n",
              "      <th>ORF_type</th>\n",
              "      <th>status</th>\n",
              "      <th>phase_score</th>\n",
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              "      <th>strand</th>\n",
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              "    <tr>\n",
              "      <th>ORF_ID</th>\n",
              "      <th></th>\n",
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              "      <th></th>\n",
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              "    <tr>\n",
              "      <th>AT4G15610.2_8909332_8909406_75</th>\n",
              "      <td>uORF</td>\n",
              "      <td>translating</td>\n",
              "      <td>0.855545</td>\n",
              "      <td>746</td>\n",
              "      <td>75</td>\n",
              "      <td>25</td>\n",
              "      <td>1.0</td>\n",
              "      <td>29.840000</td>\n",
              "      <td>AT4G15610.2</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>AT4G15610</td>\n",
              "      <td>AT4G15610</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>4</td>\n",
              "      <td>+</td>\n",
              "      <td>ATT</td>\n",
              "      <td>[17, 2, 4, 21, 3, 2, 11, 12, 0, 16, 3, 1, 8, 4...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>AT1G68530.2_25712993_25713052_60</th>\n",
              "      <td>dORF</td>\n",
              "      <td>translating</td>\n",
              "      <td>0.819610</td>\n",
              "      <td>199</td>\n",
              "      <td>60</td>\n",
              "      <td>20</td>\n",
              "      <td>1.0</td>\n",
              "      <td>9.950000</td>\n",
              "      <td>AT1G68530.2</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>AT1G68530</td>\n",
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              "      <td>-</td>\n",
              "      <td>AGG</td>\n",
              "      <td>[12, 3, 1, 10, 1, 1, 5, 7, 1, 6, 1, 2, 3, 0, 4...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>AT5G48485.1_19646320_19646625_306</th>\n",
              "      <td>annotated</td>\n",
              "      <td>translating</td>\n",
              "      <td>0.803626</td>\n",
              "      <td>2094</td>\n",
              "      <td>306</td>\n",
              "      <td>102</td>\n",
              "      <td>1.0</td>\n",
              "      <td>20.529412</td>\n",
              "      <td>AT5G48485.1</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>AT5G48485</td>\n",
              "      <td>DIR1</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>5</td>\n",
              "      <td>-</td>\n",
              "      <td>ATG</td>\n",
              "      <td>[9, 0, 4, 0, 0, 1, 1, 1, 4, 6, 5, 6, 0, 0, 1, ...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>AT1G60950.1_22444565_22445008_444</th>\n",
              "      <td>annotated</td>\n",
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              "      <td>0.861726</td>\n",
              "      <td>7208</td>\n",
              "      <td>444</td>\n",
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              "      <td>AT1G60950</td>\n",
              "      <td>FD2</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>1</td>\n",
              "      <td>+</td>\n",
              "      <td>ATG</td>\n",
              "      <td>[55, 2, 9, 6, 3, 11, 4, 4, 33, 3, 7, 26, 5, 3,...</td>\n",
              "    </tr>\n",
              "    <tr>\n",
              "      <th>AT1G62660.2_23200187_23200300_114</th>\n",
              "      <td>uORF</td>\n",
              "      <td>translating</td>\n",
              "      <td>0.821548</td>\n",
              "      <td>589</td>\n",
              "      <td>114</td>\n",
              "      <td>38</td>\n",
              "      <td>1.0</td>\n",
              "      <td>15.500000</td>\n",
              "      <td>AT1G62660.2</td>\n",
              "      <td>protein_coding</td>\n",
              "      <td>AT1G62660</td>\n",
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              "      <td>+</td>\n",
              "      <td>ACG</td>\n",
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            ]
          },
          "metadata": {},
          "execution_count": 6
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "# Load profile from the first uORF\n",
        "profile = eval(ribotricer_df.loc['AT4G15610.2_8909332_8909406_75', 'profile'])\n",
        "plot_framewise_counts(pd.Series(profile, index=range(1, len(profile)+1)))"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 314
        },
        "id": "iYJxXQrT1xQJ",
        "outputId": "ad996c5d-eb01-4f69-f783-e42f28786fd9"
      },
      "execution_count": 7,
      "outputs": [
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "<AxesSubplot:ylabel='Number of reads'>"
            ]
          },
          "metadata": {},
          "execution_count": 7
        },
        {
          "output_type": "display_data",
          "data": {
            "text/plain": [
              "<Figure size 432x288 with 1 Axes>"
            ],
            "image/png": 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\n"
          },
          "metadata": {
            "needs_background": "light"
          }
        }
      ]
    }
  ]
}