ProtamineAnalysis.ipynb

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   "source": [
    "#!/usr/bin/python3\n",
    "#\n",
    "#   Written by Christian D. Powell, 10/14/2019\n",
    "#   Copyright (c) 2019. Christian D. Powell and Hunter N.B. Moseley\n",
    "#   All rights reserved.\n",
    "#\n",
    "#   Python Notebook used to generate image files for publication.\n",
    "\n",
    "from copy import deepcopy\n",
    "import jsonpickle\n",
    "from math import log2\n",
    "import numpy as np\n",
    "import plotly.graph_objs as go\n",
    "from plotly.offline import init_notebook_mode\n",
    "from ProtamineAnalysis import *\n",
    "from scipy.stats import ttest_ind\n",
    "init_notebook_mode(connected=True)\n",
    "\n",
    "AMINOACIDS = (\n",
    "    'A', 'Q', 'L', 'S',\n",
    "    'E', 'K', 'T',\n",
    "    'N', 'G', 'M', 'W',\n",
    "    'D', 'H', 'F', 'Y',\n",
    "    'C', 'I', 'P', 'V',\n",
    "    'B', 'Z', 'X',\n",
    ")"
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    "#\n",
    "#   Open Datasets\n",
    "#\n",
    "\n",
    "with open('Docs/Datasets/eutherian_p1.json', 'r') as f:\n",
    "    ep1_align = jsonpickle.decode(f.read())\n",
    "with open('Docs/Datasets/eutherian_p2.json', 'r') as f:\n",
    "    ep2_align = jsonpickle.decode(f.read())\n",
    "with open('Docs/Datasets/metatherian.json', 'r') as f:\n",
    "    mp1_align = jsonpickle.decode(f.read())\n",
    "with open('Docs/Datasets/fish.json', 'r') as f:\n",
    "    fish_align = jsonpickle.decode(f.read())\n",
    "alignments = [ep1_align, ep2_align, mp1_align, fish_align]"
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       "                        {\"responsive\": true}\n",
       "                    ).then(function(){\n",
       "                            \n",
       "var gd = document.getElementById('f45ed43c-14fc-4d28-a3c0-5b6b867bd07b');\n",
       "var x = new MutationObserver(function (mutations, observer) {{\n",
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       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
       "        }}\n",
       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
       "}}\n",
       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
       "}}\n",
       "\n",
       "                        })\n",
       "                };\n",
       "                });\n",
       "            </script>\n",
       "        </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#\n",
    "#   Figure 5. Arginine-Lysine Residues\n",
    "#\n",
    "#   Box plots of the arginine frequency for eutherian protamine P1, truncated eutherian P2, metatherian P1, and\n",
    "#   fish protamines. Individual arginine-lysine frequencies are plotted next to the associated box plot.\n",
    "#\n",
    "#   Note: Plotly uses 1.5 IQR to determine lower (https://help.plot.ly/what-is-a-box-plot/)\n",
    "\n",
    "ep1_RK_freqs = [analysis.frequency(pro, ['R', 'K']) for pro in ep1_align.protein_list]\n",
    "ep2_RK_freqs = [analysis.frequency(pro, ['R', 'K']) for pro in ep2_align.protein_list]\n",
    "ep2T_RK_freqs = analysis.region_frequencies(ep2_align, ['R', 'K'], 48)\n",
    "mp1_RK_freqs = [analysis.frequency(pro, ['R', 'K']) for pro in mp1_align.protein_list]\n",
    "fish_RK_freqs = [analysis.frequency(pro, ['R', 'K']) for pro in fish_align.protein_list]\n",
    "\n",
    "data = [\n",
    "    go.Box(y=ep1_RK_freqs, name='Eutherian P1', boxpoints='all'),\n",
    "    go.Box(y=ep2_RK_freqs, name='Eutherian P2', boxpoints='all'),\n",
    "    go.Box(y=ep2T_RK_freqs, name='Truncated Eutherian P2', boxpoints='all'),\n",
    "    go.Box(y=mp1_RK_freqs, name='Metatherian', boxpoints='all'),\n",
    "    go.Box(y=fish_RK_freqs, name='Fish', boxpoints='all'),\n",
    "]\n",
    "charge_freq_layout = go.Layout(xaxis=dict(title='Protamine Type'),\n",
    "                               yaxis=dict(title='Arginine-Lysine Frequency (%)'),\n",
    "                               showlegend=False)\n",
    "fig = go.Figure(data=data, layout=charge_freq_layout)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
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       "                        {\"responsive\": true}\n",
       "                    ).then(function(){\n",
       "                            \n",
       "var gd = document.getElementById('0455f0e7-e8ea-4256-9d40-ac3a8aa5e459');\n",
       "var x = new MutationObserver(function (mutations, observer) {{\n",
       "        var display = window.getComputedStyle(gd).display;\n",
       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
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       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
       "}}\n",
       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
       "}}\n",
       "\n",
       "                        })\n",
       "                };\n",
       "                });\n",
       "            </script>\n",
       "        </div>"
      ]
     },
     "metadata": {},
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   ],
   "source": [
    "#\n",
    "#   Arginine-Lysine Residues (DNA Binding)\n",
    "#\n",
    "#   Box plots of the arginine frequency for eutherian P1, eutherian P1 DNA binding region, metatherian P1, \n",
    "#   metatherian P1 DNA binding region, fish protamines (for comparison only). Individual arginine-lysine \n",
    "#   frequencies are plotted next to the associated box plot.\n",
    "#\n",
    "#   Note: Plotly uses 1.5 IQR to determine lower (https://help.plot.ly/what-is-a-box-plot/)\n",
    "\n",
    "ep1DNA_RK_freqs = analysis.region_frequencies(ep1_align, ['R', 'K'], 17, 48)\n",
    "mp1DNA_RK_freqs = analysis.region_frequencies(mp1_align, ['R', 'K'], 17, 56)\n",
    "\n",
    "data = [\n",
    "    go.Box(y=ep1_RK_freqs, name='Eutherian P1', boxpoints='all'),\n",
    "    go.Box(y=ep1DNA_RK_freqs, name='Eutherian P1 DNA', boxpoints='all'),\n",
    "    go.Box(y=mp1_RK_freqs, name='Metatherian', boxpoints='all'),\n",
    "    go.Box(y=mp1DNA_RK_freqs, name='Metatherian DNA', boxpoints='all'),\n",
    "    go.Box(y=fish_RK_freqs, name='Fish', boxpoints='all'),\n",
    "]\n",
    "charge_freq_layout = go.Layout(xaxis=dict(title='Protamine Type'),\n",
    "                               yaxis=dict(title='Arginine-Lysine Frequency (%)'),\n",
    "                               showlegend=False)\n",
    "fig = go.Figure(data=data, layout=charge_freq_layout)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
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     "output_type": "display_data"
    }
   ],
   "source": [
    "#\n",
    "#   Figure 6. Arginine-Lysine Residues (DNA Binding ONLY)\n",
    "#\n",
    "#   Box plots of the arginine-lysine frequency for the DNA binding regions of eutherian protamine P1, metatherian\n",
    "#   sperm protamine, and the whole sequences of fish protamines. Individual arginine-lysine frequencies are\n",
    "#   plotted next to the associated box plot.\n",
    "#\n",
    "#   Note: Plotly uses 1.5 IQR to determine lower (https://help.plot.ly/what-is-a-box-plot/)\n",
    "\n",
    "data = [\n",
    "    go.Box(y=ep1DNA_RK_freqs, name='Eutherian P1 DNA', boxpoints='all'),\n",
    "    go.Box(y=mp1DNA_RK_freqs, name='Metatherian DNA', boxpoints='all'),\n",
    "    go.Box(y=fish_RK_freqs, name='Fish', boxpoints='all'),\n",
    "]\n",
    "charge_freq_layout = go.Layout(xaxis=dict(title='Protamine Type'),\n",
    "                               yaxis=dict(title='Arginine-Lysine Frequency (%)'),\n",
    "                               showlegend=False)\n",
    "fig = go.Figure(data=data, layout=charge_freq_layout)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "#\n",
    "#   Figures below not used in publication\n",
    "#"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
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   "source": [
    "#\n",
    "#   Arginine Residue Frequency\n",
    "#\n",
    "#   Box plots of the arginine frequency for each protmaine group. Eutherian P1, Eutherian P2, Truncated Eutherian\n",
    "#   P2, Metatherian, and fish. Individual arginine frequencies are plotted next to the associated box plot.\n",
    "#\n",
    "#   Note: Plotly uses 1.5 IQR to determine lower (https://help.plot.ly/what-is-a-box-plot/)\n",
    "\n",
    "ep1_R_freqs = [analysis.frequency(pro, 'R') for pro in ep1_align.protein_list]\n",
    "ep2_R_freqs = [analysis.frequency(pro, 'R') for pro in ep2_align.protein_list]\n",
    "ep2T_R_freqs = analysis.region_frequencies(ep2_align, ['R'], 48)\n",
    "mp1_R_freqs = [analysis.frequency(pro, 'R') for pro in mp1_align.protein_list]\n",
    "fish_R_freqs = [analysis.frequency(pro, 'R') for pro in fish_align.protein_list]\n",
    "\n",
    "data = [\n",
    "    go.Box(y=ep1_R_freqs, name='Eutherian P1', boxpoints='all'),\n",
    "    go.Box(y=ep2_R_freqs, name='Eutherian P2', boxpoints='all'),\n",
    "    go.Box(y=ep2T_R_freqs, name='Truncated Eutherian P2', boxpoints='all'),\n",
    "    go.Box(y=mp1_R_freqs, name='Metatherian', boxpoints='all'),\n",
    "    go.Box(y=fish_R_freqs, name='Fish', boxpoints='all'),\n",
    "]\n",
    "charge_freq_layout = go.Layout(xaxis=dict(title='Protamine Type'),\n",
    "                               yaxis=dict(title='Arginine Frequency (%)'),\n",
    "                               showlegend=False)\n",
    "fig = go.Figure(data=data, layout=charge_freq_layout)\n",
    "fig.show()"
   ]
  },
  {
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   "execution_count": 8,
   "metadata": {},
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     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#\n",
    "#   Arginine Residue Frequency (Eutherian P1 DNA Binding Region)\n",
    "#\n",
    "#   Box plots of the arginine frequency for each protamine group. Eutherian P1, Eutherian P1 DNA binding region,\n",
    "#   Metatherian, and fish. Individual arginine frequencies are plotted next to the associated box plot.\n",
    "#\n",
    "#   Note: Plotly uses 1.5 IQR to determine lower (https://help.plot.ly/what-is-a-box-plot/)\n",
    "\n",
    "ep1DNA_R_freq = analysis.region_frequencies(ep1_align, ['R'], 17, 48)\n",
    "\n",
    "data = [\n",
    "    go.Box(y=ep1_R_freqs, name='Eutherian P1', boxpoints='all'),\n",
    "    go.Box(y=ep1DNA_R_freq, name='Eutherian P1 DNA', boxpoints='all'),\n",
    "    go.Box(y=mp1_R_freqs, name='Metatherian', boxpoints='all'),\n",
    "    go.Box(y=fish_R_freqs, name='Fish', boxpoints='all'),\n",
    "]\n",
    "charge_freq_layout = go.Layout(xaxis=dict(title='Protamine Type'),\n",
    "                               yaxis=dict(title='Arginine Frequency (%)'),\n",
    "                               showlegend=False)\n",
    "fig = go.Figure(data=data, layout=charge_freq_layout)\n",
    "fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
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       "                        {\"responsive\": true}\n",
       "                    ).then(function(){\n",
       "                            \n",
       "var gd = document.getElementById('49c64478-6f29-48e6-8a39-38441ae7d273');\n",
       "var x = new MutationObserver(function (mutations, observer) {{\n",
       "        var display = window.getComputedStyle(gd).display;\n",
       "        if (!display || display === 'none') {{\n",
       "            console.log([gd, 'removed!']);\n",
       "            Plotly.purge(gd);\n",
       "            observer.disconnect();\n",
       "        }}\n",
       "}});\n",
       "\n",
       "// Listen for the removal of the full notebook cells\n",
       "var notebookContainer = gd.closest('#notebook-container');\n",
       "if (notebookContainer) {{\n",
       "    x.observe(notebookContainer, {childList: true});\n",
       "}}\n",
       "\n",
       "// Listen for the clearing of the current output cell\n",
       "var outputEl = gd.closest('.output');\n",
       "if (outputEl) {{\n",
       "    x.observe(outputEl, {childList: true});\n",
       "}}\n",
       "\n",
       "                        })\n",
       "                };\n",
       "                });\n",
       "            </script>\n",
       "        </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#\n",
    "#   Variance Analysis (Eutherian P1 DNA Binding Region)\n",
    "#\n",
    "#   Note: Plotly uses 1.5 IQR to determine lower (https://help.plot.ly/what-is-a-box-plot/)\n",
    "\n",
    "for alignment in alignments:\n",
    "    aa_ranges = list()\n",
    "\n",
    "    for aa in AMINOACIDS:\n",
    "        new_freq = [analysis.frequency(pro, ['R', aa]) for pro in alignment.protein_list]\n",
    "        aa_ranges.append(new_freq)\n",
    "        print(aa, max(new_freq) - min(new_freq), np.percentile(new_freq, [0, 25, 50, 75, 100]))\n",
    "\n",
    "    low = aa_ranges[0]\n",
    "    for x in range(1, len(aa_ranges)):\n",
    "        if max(aa_ranges[x]) - min(aa_ranges[x]) < max(low) - min(low):\n",
    "            low = aa_ranges[x]\n",
    "\n",
    "    print(aa_ranges.index(low), np.percentile(low, [0, 25, 50, 75, 100]), '\\n',\n",
    "          np.percentile(aa_ranges[4], [0, 25, 50, 75, 100]))\n",
    "\n",
    "    data = [go.Box(y=val, name=AMINOACIDS[i], boxpoints='all') for i, val in enumerate(aa_ranges)]\n",
    "    charge_freq_layout = go.Layout(xaxis=dict(title='R + ?'),\n",
    "                                   yaxis=dict(title='Charge Frequency (%)'))\n",
    "    fig = go.Figure(data=data, layout=charge_freq_layout)\n",
    "    fig.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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