Converting_rds_to_pandas.ipynb

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      "name": "Converting .rds to pandas.ipynb",
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        "<a href=\"https://colab.research.google.com/github/petermr/CEVOpen/blob/master/Converting_rds_to_pandas.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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      "source": [
        "##**Convert .rds files to Pandas**\n",
        "To save a single R object in a file, we use .rds. While Pandas is a library used for data manipulation in Python.\n",
        "\n",
        "The following code changes .rds files to Panads. This helps to run R files in Python using pyreadr."
      ],
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          "text": [
            "Cloning into 'pfocr-curation-terpene-edition'...\n",
            "remote: Enumerating objects: 13, done.\u001b[K\n",
            "remote: Counting objects: 100% (13/13), done.\u001b[K\n",
            "remote: Compressing objects: 100% (13/13), done.\u001b[K\n",
            "remote: Total 13 (delta 3), reused 6 (delta 0), pack-reused 0\u001b[K\n",
            "Unpacking objects: 100% (13/13), done.\n"
          ]
        }
      ],
      "source": [
        "!git clone https://github.com/wikipathways/pfocr-curation-terpene-edition.git\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install pyreadr"
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          "name": "stdout",
          "text": [
            "Requirement already satisfied: pyreadr in /usr/local/lib/python3.7/dist-packages (0.4.4)\n",
            "Requirement already satisfied: pandas>=1.2.0 in /usr/local/lib/python3.7/dist-packages (from pyreadr) (1.3.5)\n",
            "Requirement already satisfied: pytz>=2017.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.2.0->pyreadr) (2018.9)\n",
            "Requirement already satisfied: numpy>=1.17.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.2.0->pyreadr) (1.19.5)\n",
            "Requirement already satisfied: python-dateutil>=2.7.3 in /usr/local/lib/python3.7/dist-packages (from pandas>=1.2.0->pyreadr) (2.8.2)\n",
            "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.7/dist-packages (from python-dateutil>=2.7.3->pandas>=1.2.0->pyreadr) (1.15.0)\n"
          ]
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    {
      "cell_type": "code",
      "source": [
        "import pyreadr\n",
        "result = pyreadr.read_r('/content/pfocr-curation-terpene-edition/pfocr_curating_terpene.rds') # also works for RData\n",
        "print(result)\n",
        "# done! \n",
        "# result is a dictionary where keys are the name of objects and the values python\n",
        "# objects. In the case of Rds there is only one object with None as key\n",
        "df = result[None]"
      ],
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          "text": [
            "OrderedDict([(None,                                                  figid  ...                                            caption\n",
            "0                         PMC1183420__pp1382344f01.jpg  ...  Simplified 13-hydroxylation pathway of GA bios...\n",
            "1                          PMC122160__pq0326589001.jpg  ...  The nonmevalonate pathway of isoprenoid biosyn...\n",
            "2                         PMC1256006__pp1390920f02.jpg  ...  Isoprenoid biosynthetic pathway in higher plan...\n",
            "3                         PMC1283772__pp1391366f01.jpg  ...  Overview of the GA biosynthetic pathway. The a...\n",
            "4                         PMC1361334__pp1400681f01.jpg  ...  A scheme of stimulus-responsive isoprenoid bio...\n",
            "..                                                 ...  ...                                                ...\n",
            "345  PMC6879371__plantbiotechnology-35-3-18.0601a-f...  ...                                                NaN\n",
            "346  PMC6879386__plantbiotechnology-35-2-18.0324a-f...  ...                                                NaN\n",
            "347  PMC6902898__Beilstein_J_Org_Chem-15-2889-g012.jpg  ...  Engineering of terpenoid pathways. a) Metaboli...\n",
            "348       PMC6921081__microorganisms-07-00560-g005.jpg  ...  Proposed pathway for epoxy-janthitrem I–IV bio...\n",
            "349              PMC6955855__insects-10-00441-g005.jpg  ...  Terpene and terpenoids biosynthesis. The precu...\n",
            "\n",
            "[350 rows x 13 columns])])\n"
          ]
        }
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      "source": [
        "import pandas as pd\n",
        "##r=result[figid]\n",
        "data=pd.DataFrame(df)\n",
        "data\n"
      ],
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              "      <td>Jon Anders Stavang, et al.</td>\n",
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              "      <td>NULL</td>\n",
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              "      <td>PMC1283772__pp1391366f01.jpg</td>\n",
              "      <td>PMC1283772</td>\n",
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              "      <td>pp1391366f01.jpg</td>\n",
              "      <td>/pmc/articles/PMC1283772/figure/fig1/</td>\n",
              "      <td>NULL</td>\n",
              "      <td>NULL</td>\n",
              "      <td>2005</td>\n",
              "      <td>Sam Lievens, et al.</td>\n",
              "      <td>Gibberellins Are Involved in Nodulation of Ses...</td>\n",
              "      <td>Overview of the GA biosynthetic pathway</td>\n",
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              "      <th>4</th>\n",
              "      <td>PMC1361334__pp1400681f01.jpg</td>\n",
              "      <td>PMC1361334</td>\n",
              "      <td>Chihiro Yamamizo, et al. Plant Physiol. 2006 F...</td>\n",
              "      <td>pp1400681f01.jpg</td>\n",
              "      <td>/pmc/articles/PMC1361334/figure/fig1/</td>\n",
              "      <td>NULL</td>\n",
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              "      <td>2006</td>\n",
              "      <td>Chihiro Yamamizo, et al.</td>\n",
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              "      <td>A scheme of stimulus-responsive isoprenoid bio...</td>\n",
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              "      <td>2018-09-01</td>\n",
              "      <td>Plant biotechnology (Tokyo, Japan)</td>\n",
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              "      <td>Hidenobu Uchida, Eiichi Mizohata, Shigeru Okada</td>\n",
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              "      <td>PMC6879386</td>\n",
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              "      <td>/pmc/articles/PMC6879386/figure/figure1/</td>\n",
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              "      <td>/pmc/articles/PMC6902898/figure/F11/</td>\n",
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              "      <td>Emma J Ludlow, Simone Vassiliadis, Piyumi N Ek...</td>\n",
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              "      <td>PMC6955855</td>\n",
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              "      <td>/pmc/articles/PMC6955855/figure/insects-10-004...</td>\n",
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              "      <td>2019</td>\n",
              "      <td>Matteo Calcagnile, Salvatore Maurizio SM Tredi...</td>\n",
              "      <td>Bacterial Semiochemicals and Transkingdom Inte...</td>\n",
              "      <td>Terpene and terpenoids biosynthesis</td>\n",
              "      <td>Figure 5</td>\n",
              "      <td>Terpene and terpenoids biosynthesis. The precu...</td>\n",
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              "                                                 figid  ...                                            caption\n",
              "0                         PMC1183420__pp1382344f01.jpg  ...  Simplified 13-hydroxylation pathway of GA bios...\n",
              "1                          PMC122160__pq0326589001.jpg  ...  The nonmevalonate pathway of isoprenoid biosyn...\n",
              "2                         PMC1256006__pp1390920f02.jpg  ...  Isoprenoid biosynthetic pathway in higher plan...\n",
              "3                         PMC1283772__pp1391366f01.jpg  ...  Overview of the GA biosynthetic pathway. The a...\n",
              "4                         PMC1361334__pp1400681f01.jpg  ...  A scheme of stimulus-responsive isoprenoid bio...\n",
              "..                                                 ...  ...                                                ...\n",
              "345  PMC6879371__plantbiotechnology-35-3-18.0601a-f...  ...                                                NaN\n",
              "346  PMC6879386__plantbiotechnology-35-2-18.0324a-f...  ...                                                NaN\n",
              "347  PMC6902898__Beilstein_J_Org_Chem-15-2889-g012.jpg  ...  Engineering of terpenoid pathways. a) Metaboli...\n",
              "348       PMC6921081__microorganisms-07-00560-g005.jpg  ...  Proposed pathway for epoxy-janthitrem I–IV bio...\n",
              "349              PMC6955855__insects-10-00441-g005.jpg  ...  Terpene and terpenoids biosynthesis. The precu...\n",
              "\n",
              "[350 rows x 13 columns]"
            ]
          },
          "metadata": {},
          "execution_count": 9
        }
      ]
    }
  ]
}