Proteon structure prediction.ipynb

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        "<a href=\"https://colab.research.google.com/github/Ahmad162539/ML-class-excercise-codes/blob/main/Proteon%20structure%20prediction.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
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            "\n",
            "Usage:   \n",
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            "  help                        Show help for commands.\n",
            "\n",
            "General Options:\n",
            "  -h, --help\n",
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            "  otherwise.\n",
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            "  with the\n",
            "  specified\n",
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            "  used up to\n",
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            "  rresponding\n",
            "  to WARNING,\n",
            "  ERROR, and\n",
            "  CRITICAL\n",
            "  logging\n",
            "  levels).\n",
            "  --log <path>\n",
            "  Path to a\n",
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            "  appending\n",
            "  log.\n",
            "  --no-input\n",
            "  Disable\n",
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            "  (default:\n",
            "  disabled)\n",
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            "  Specify a\n",
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            "  heme://[use\n",
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            "  timeout\n",
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            "  seconds).\n",
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            "  Default\n",
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            "  See 'SSL\n",
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            "  Verificatio\n",
            "  n' in pip d\n",
            "  ocumentatio\n",
            "  n for more \n",
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            "  containing\n",
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            "  functionali\n",
            "  ty, that\n",
            "  will be\n",
            "  removed in\n",
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      "source": [
        "!pip -h"
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      "source": [
        "!pip list"
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          "text": [
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            "python-utils                  3.5.2\n",
            "pytz                          2022.7.1\n",
            "pytz-deprecation-shim         0.1.0.post0\n",
            "pyviz-comms                   2.2.1\n",
            "PyWavelets                    1.4.1\n",
            "PyYAML                        6.0\n",
            "pyzmq                         23.2.1\n",
            "qdldl                         0.1.7\n",
            "qudida                        0.0.4\n",
            "regex                         2022.10.31\n",
            "requests                      2.27.1\n",
            "requests-oauthlib             1.3.1\n",
            "requests-unixsocket           0.2.0\n",
            "requirements-parser           0.5.0\n",
            "rich                          13.3.4\n",
            "rpy2                          3.5.5\n",
            "rsa                           4.9\n",
            "scikit-image                  0.19.3\n",
            "scikit-learn                  1.2.2\n",
            "scipy                         1.10.1\n",
            "scs                           3.2.3\n",
            "seaborn                       0.12.2\n",
            "Send2Trash                    1.8.0\n",
            "setuptools                    67.7.2\n",
            "shapely                       2.0.1\n",
            "six                           1.16.0\n",
            "sklearn-pandas                2.2.0\n",
            "smart-open                    6.3.0\n",
            "sniffio                       1.3.0\n",
            "snowballstemmer               2.2.0\n",
            "sortedcontainers              2.4.0\n",
            "soundfile                     0.12.1\n",
            "soupsieve                     2.4.1\n",
            "soxr                          0.3.5\n",
            "spacy                         3.5.2\n",
            "spacy-legacy                  3.0.12\n",
            "spacy-loggers                 1.0.4\n",
            "Sphinx                        3.5.4\n",
            "sphinxcontrib-applehelp       1.0.4\n",
            "sphinxcontrib-devhelp         1.0.2\n",
            "sphinxcontrib-htmlhelp        2.0.1\n",
            "sphinxcontrib-jsmath          1.0.1\n",
            "sphinxcontrib-qthelp          1.0.3\n",
            "sphinxcontrib-serializinghtml 1.1.5\n",
            "SQLAlchemy                    2.0.10\n",
            "sqlparse                      0.4.4\n",
            "srsly                         2.4.6\n",
            "statsmodels                   0.13.5\n",
            "sympy                         1.11.1\n",
            "tables                        3.8.0\n",
            "tabulate                      0.8.10\n",
            "tblib                         1.7.0\n",
            "tenacity                      8.2.2\n",
            "tensorboard                   2.12.2\n",
            "tensorboard-data-server       0.7.0\n",
            "tensorboard-plugin-wit        1.8.1\n",
            "tensorflow                    2.12.0\n",
            "tensorflow-datasets           4.9.2\n",
            "tensorflow-estimator          2.12.0\n",
            "tensorflow-gcs-config         2.12.0\n",
            "tensorflow-hub                0.13.0\n",
            "tensorflow-io-gcs-filesystem  0.32.0\n",
            "tensorflow-metadata           1.13.1\n",
            "tensorflow-probability        0.20.1\n",
            "tensorstore                   0.1.36\n",
            "termcolor                     2.3.0\n",
            "terminado                     0.17.1\n",
            "text-unidecode                1.3\n",
            "textblob                      0.17.1\n",
            "tf-slim                       1.1.0\n",
            "thinc                         8.1.9\n",
            "threadpoolctl                 3.1.0\n",
            "tifffile                      2023.4.12\n",
            "tinycss2                      1.2.1\n",
            "toml                          0.10.2\n",
            "tomli                         2.0.1\n",
            "toolz                         0.12.0\n",
            "torch                         2.0.1+cu118\n",
            "torchaudio                    2.0.2+cu118\n",
            "torchdata                     0.6.1\n",
            "torchsummary                  1.5.1\n",
            "torchtext                     0.15.2\n",
            "torchvision                   0.15.2+cu118\n",
            "tornado                       6.3.1\n",
            "tqdm                          4.65.0\n",
            "traitlets                     5.7.1\n",
            "triton                        2.0.0\n",
            "tweepy                        4.13.0\n",
            "typer                         0.7.0\n",
            "types-setuptools              67.8.0.0\n",
            "typing_extensions             4.5.0\n",
            "tzdata                        2023.3\n",
            "tzlocal                       4.3\n",
            "uritemplate                   4.1.1\n",
            "urllib3                       1.26.15\n",
            "vega-datasets                 0.9.0\n",
            "wasabi                        1.1.1\n",
            "wcwidth                       0.2.6\n",
            "webcolors                     1.13\n",
            "webencodings                  0.5.1\n",
            "websocket-client              1.5.1\n",
            "Werkzeug                      2.3.0\n",
            "wheel                         0.40.0\n",
            "widgetsnbextension            3.6.4\n",
            "wordcloud                     1.8.2.2\n",
            "wrapt                         1.14.1\n",
            "xarray                        2022.12.0\n",
            "xarray-einstats               0.5.1\n",
            "xgboost                       1.7.5\n",
            "xlrd                          2.0.1\n",
            "yellowbrick                   1.5\n",
            "yfinance                      0.2.18\n",
            "zict                          3.0.0\n",
            "zipp                          3.15.0\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install biopython"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "LlExwDkreYyw",
        "outputId": "14fb9054-3efb-4d8f-c613-fe8e1e3c505d"
      },
      "execution_count": null,
      "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 biopython\n",
            "  Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)\n",
            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.1/3.1 MB\u001b[0m \u001b[31m30.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hRequirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython) (1.22.4)\n",
            "Installing collected packages: biopython\n",
            "Successfully installed biopython-1.81\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "gmyiei2hevP5",
        "outputId": "a0c94b64-f86b-4753-ad41-931072caa502"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2023-05-24 06:39:36--  https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n",
            "Resolving repo.anaconda.com (repo.anaconda.com)... 104.16.131.3, 104.16.130.3, 2606:4700::6810:8303, ...\n",
            "Connecting to repo.anaconda.com (repo.anaconda.com)|104.16.131.3|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 73134376 (70M) [application/x-sh]\n",
            "Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’\n",
            "\n",
            "Miniconda3-latest-L 100%[===================>]  69.75M   211MB/s    in 0.3s    \n",
            "\n",
            "2023-05-24 06:39:37 (211 MB/s) - ‘Miniconda3-latest-Linux-x86_64.sh’ saved [73134376/73134376]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "aQBOi4k1fEGg",
        "outputId": "0b265ebc-3647-442c-a11e-f1c690a1df01"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": []
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!conda env list"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "obaegBzlfZII",
        "outputId": "1520f453-3bf4-4673-dd93-d2974bf485ae"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "# conda environments:\n",
            "#\n",
            "base                     /usr/local\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!conda list"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Nyu9FvLhfuLZ",
        "outputId": "e4325c75-0882-4f8b-e007-d2e1ee1591aa"
      },
      "execution_count": null,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "# packages in environment at /usr/local:\n",
            "#\n",
            "# Name                    Version                   Build  Channel\n",
            "_libgcc_mutex             0.1                        main  \n",
            "_openmp_mutex             5.1                       1_gnu  \n",
            "boltons                   23.0.0          py310h06a4308_0  \n",
            "brotlipy                  0.7.0           py310h7f8727e_1002  \n",
            "bzip2                     1.0.8                h7b6447c_0  \n",
            "ca-certificates           2023.01.10           h06a4308_0  \n",
            "certifi                   2022.12.7       py310h06a4308_0  \n",
            "cffi                      1.15.1          py310h5eee18b_3  \n",
            "charset-normalizer        2.0.4              pyhd3eb1b0_0  \n",
            "conda                     23.3.1          py310h06a4308_0  \n",
            "conda-content-trust       0.1.3           py310h06a4308_0  \n",
            "conda-package-handling    2.0.2           py310h06a4308_0  \n",
            "conda-package-streaming   0.7.0           py310h06a4308_0  \n",
            "cryptography              39.0.1          py310h9ce1e76_0  \n",
            "idna                      3.4             py310h06a4308_0  \n",
            "jsonpatch                 1.32               pyhd3eb1b0_0  \n",
            "jsonpointer               2.1                pyhd3eb1b0_0  \n",
            "ld_impl_linux-64          2.38                 h1181459_1  \n",
            "libffi                    3.4.2                h6a678d5_6  \n",
            "libgcc-ng                 11.2.0               h1234567_1  \n",
            "libgomp                   11.2.0               h1234567_1  \n",
            "libstdcxx-ng              11.2.0               h1234567_1  \n",
            "libuuid                   1.41.5               h5eee18b_0  \n",
            "ncurses                   6.4                  h6a678d5_0  \n",
            "openssl                   1.1.1t               h7f8727e_0  \n",
            "packaging                 23.0            py310h06a4308_0  \n",
            "pip                       23.0.1          py310h06a4308_0  \n",
            "pluggy                    1.0.0           py310h06a4308_1  \n",
            "pycosat                   0.6.4           py310h5eee18b_0  \n",
            "pycparser                 2.21               pyhd3eb1b0_0  \n",
            "pyopenssl                 23.0.0          py310h06a4308_0  \n",
            "pysocks                   1.7.1           py310h06a4308_0  \n",
            "python                    3.10.10              h7a1cb2a_2  \n",
            "readline                  8.2                  h5eee18b_0  \n",
            "requests                  2.28.1          py310h06a4308_1  \n",
            "ruamel.yaml               0.17.21         py310h5eee18b_0  \n",
            "ruamel.yaml.clib          0.2.6           py310h5eee18b_1  \n",
            "setuptools                65.6.3          py310h06a4308_0  \n",
            "six                       1.16.0             pyhd3eb1b0_1  \n",
            "sqlite                    3.41.1               h5eee18b_0  \n",
            "tk                        8.6.12               h1ccaba5_0  \n",
            "toolz                     0.12.0          py310h06a4308_0  \n",
            "tqdm                      4.65.0          py310h2f386ee_0  \n",
            "tzdata                    2023c                h04d1e81_0  \n",
            "urllib3                   1.26.15         py310h06a4308_0  \n",
            "wheel                     0.38.4          py310h06a4308_0  \n",
            "xz                        5.2.10               h5eee18b_1  \n",
            "zlib                      1.2.13               h5eee18b_0  \n",
            "zstandard                 0.19.0          py310h5eee18b_0  \n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!pip install biopython"
      ],
      "metadata": {
        "id": "f83XxebXfylg",
        "outputId": "7e3bfa6b-3234-4413-c727-2ba36ea6e5b3",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 1,
      "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 biopython\n",
            "  Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)\n",
            "\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.1/3.1 MB\u001b[0m \u001b[31m31.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
            "\u001b[?25hRequirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython) (1.22.4)\n",
            "Installing collected packages: biopython\n",
            "Successfully installed biopython-1.81\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://rest.uniprot.org/uniprotkb/P0A6V8.fasta"
      ],
      "metadata": {
        "id": "ZNc5-iHlrKrB",
        "outputId": "0a4a7013-42f4-42af-cabf-c61b047b0360",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 2,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2023-05-24 07:33:38--  https://rest.uniprot.org/uniprotkb/P0A6V8.fasta\n",
            "Resolving rest.uniprot.org (rest.uniprot.org)... 193.62.193.81\n",
            "Connecting to rest.uniprot.org (rest.uniprot.org)|193.62.193.81|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 419 [text/plain]\n",
            "Saving to: ‘P0A6V8.fasta’\n",
            "\n",
            "P0A6V8.fasta        100%[===================>]     419  --.-KB/s    in 0s      \n",
            "\n",
            "2023-05-24 07:33:39 (114 MB/s) - ‘P0A6V8.fasta’ saved [419/419]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "from Bio import SeqIO\n",
        "target = SeqIO.read(\"P0A6V8.fasta\", \"fasta\")\n",
        "query_sequence = str (target.seq)\n",
        "jobname= target.description\n",
        "print(f\"its seuence is ...{jobname}\")\n"
      ],
      "metadata": {
        "id": "wqTEpLYtraUE",
        "outputId": "0e15189a-019a-43c5-e1c4-2f8deac7809b",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 3,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "its seuence is ...sp|P0A6V8|GLK_ECOLI Glucokinase OS=Escherichia coli (strain K12) OX=83333 GN=glk PE=1 SV=1\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!wget https://rest.uniprot.org/uniprotkb/B7V9H3.fasta"
      ],
      "metadata": {
        "id": "PdthUFGHr8vT",
        "outputId": "e42d7b52-8d3d-4a25-b6c0-99676366ef77",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 4,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "--2023-05-24 07:42:14--  https://rest.uniprot.org/uniprotkb/B7V9H3.fasta\n",
            "Resolving rest.uniprot.org (rest.uniprot.org)... 193.62.193.81\n",
            "Connecting to rest.uniprot.org (rest.uniprot.org)|193.62.193.81|:443... connected.\n",
            "HTTP request sent, awaiting response... 200 OK\n",
            "Length: 439 [text/plain]\n",
            "Saving to: ‘B7V9H3.fasta’\n",
            "\n",
            "B7V9H3.fasta        100%[===================>]     439  --.-KB/s    in 0s      \n",
            "\n",
            "2023-05-24 07:42:15 (101 MB/s) - ‘B7V9H3.fasta’ saved [439/439]\n",
            "\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!cat P0A6V8.fasta B7V9H3.fasta > query.fasta"
      ],
      "metadata": {
        "id": "jHqtdGy4taCS"
      },
      "execution_count": 5,
      "outputs": []
    },
    {
      "cell_type": "code",
      "source": [
        "!sudo apt update\n",
        "!sudo apt install kalign\n",
        "!conda install -y -q -c bioconda kalign2=2.04 python=3.7 2>&1 1>/dev/null"
      ],
      "metadata": {
        "id": "6ZWG-x9rth17",
        "outputId": "aeefe96f-1ba4-416c-b740-10da8a72009a",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 10,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\u001b[33m\r0% [Working]\u001b[0m\r            \rGet:1 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease [3,622 B]\n",
            "Hit:2 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  InRelease\n",
            "Get:3 http://security.ubuntu.com/ubuntu focal-security InRelease [114 kB]\n",
            "Hit:4 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease\n",
            "Hit:5 http://archive.ubuntu.com/ubuntu focal InRelease\n",
            "Get:6 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]\n",
            "Hit:7 http://ppa.launchpad.net/cran/libgit2/ubuntu focal InRelease\n",
            "Get:8 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal InRelease [18.1 kB]\n",
            "Get:9 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [1,050 kB]\n",
            "Get:10 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]\n",
            "Get:11 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1,345 kB]\n",
            "Hit:12 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu focal InRelease\n",
            "Hit:13 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu focal InRelease\n",
            "Get:14 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [2,726 kB]\n",
            "Get:15 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [3,202 kB]\n",
            "Get:16 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal/main amd64 Packages [29.5 kB]\n",
            "Get:17 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [2,270 kB]\n",
            "Get:18 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]\n",
            "Get:19 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [28.6 kB]\n",
            "Fetched 11.1 MB in 3s (4,256 kB/s)\n",
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
            "Reading state information... Done\n",
            "33 packages can be upgraded. Run 'apt list --upgradable' to see them.\n",
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
            "Reading state information... Done\n",
            "The following NEW packages will be installed:\n",
            "  kalign\n",
            "0 upgraded, 1 newly installed, 0 to remove and 33 not upgraded.\n",
            "Need to get 93.1 kB of archives.\n",
            "After this operation, 259 kB of additional disk space will be used.\n",
            "Get:1 http://archive.ubuntu.com/ubuntu focal/universe amd64 kalign amd64 1:2.03+20110620-5 [93.1 kB]\n",
            "Fetched 93.1 kB in 1s (133 kB/s)\n",
            "debconf: unable to initialize frontend: Dialog\n",
            "debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76, <> line 1.)\n",
            "debconf: falling back to frontend: Readline\n",
            "debconf: unable to initialize frontend: Readline\n",
            "debconf: (This frontend requires a controlling tty.)\n",
            "debconf: falling back to frontend: Teletype\n",
            "dpkg-preconfigure: unable to re-open stdin: \n",
            "Selecting previously unselected package kalign.\n",
            "(Reading database ... 122532 files and directories currently installed.)\n",
            "Preparing to unpack .../kalign_1%3a2.03+20110620-5_amd64.deb ...\n",
            "Unpacking kalign (1:2.03+20110620-5) ...\n",
            "Setting up kalign (1:2.03+20110620-5) ...\n",
            "Processing triggers for man-db (2.9.1-1) ...\n",
            "/bin/bash: conda: command not found\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "!sudo apt update\n",
        "!sudo apt install kalign\n",
        "!kalign query.fasta query_out.a3m"
      ],
      "metadata": {
        "id": "9VZVBW1Gtz4X",
        "outputId": "f4035c22-853a-4d01-c61c-9f65028167a1",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 11,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "\u001b[33m\r0% [Working]\u001b[0m\r            \rHit:1 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease\n",
            "\u001b[33m\r0% [Connecting to archive.ubuntu.com (185.125.190.39)] [Connecting to security.\u001b[0m\r                                                                               \rHit:2 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  InRelease\n",
            "\u001b[33m\r0% [Connecting to archive.ubuntu.com (185.125.190.39)] [Connecting to security.\u001b[0m\u001b[33m\r                                                                               \r0% [Waiting for headers] [Waiting for headers] [Waiting for headers]\u001b[0m\u001b[33m\r0% [Waiting for headers] [Waiting for headers] [Waiting for headers]\u001b[0m\r                                                                    \rHit:3 http://archive.ubuntu.com/ubuntu focal InRelease\n",
            "\u001b[33m\r0% [Waiting for headers] [Waiting for headers] [Waiting for headers]\u001b[0m\r                                                                    \rHit:4 http://security.ubuntu.com/ubuntu focal-security InRelease\n",
            "Hit:5 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease\n",
            "Hit:6 http://archive.ubuntu.com/ubuntu focal-updates InRelease\n",
            "Hit:7 http://archive.ubuntu.com/ubuntu focal-backports InRelease\n",
            "Hit:8 http://ppa.launchpad.net/cran/libgit2/ubuntu focal InRelease\n",
            "Hit:9 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal InRelease\n",
            "Hit:10 http://ppa.launchpad.net/graphics-drivers/ppa/ubuntu focal InRelease\n",
            "Hit:11 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu focal InRelease\n",
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
            "Reading state information... Done\n",
            "33 packages can be upgraded. Run 'apt list --upgradable' to see them.\n",
            "Reading package lists... Done\n",
            "Building dependency tree       \n",
            "Reading state information... Done\n",
            "kalign is already the newest version (1:2.03+20110620-5).\n",
            "0 upgraded, 0 newly installed, 0 to remove and 33 not upgraded.\n",
            "EXTRA :2\n",
            "\n",
            "Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann\n",
            "\n",
            "        Kalign is free software. You can redistribute it and/or modify\n",
            "        it under the terms of the GNU General Public License as\n",
            "        published by the Free Software Foundation.\n",
            "\n",
            "reading from STDIN: found no sequences.\n",
            "\n",
            "reading from query.fasta: found 2 sequences\n",
            "reading from query_out.a3m: found no sequences.\n",
            "-> output file, in fasta format\n",
            "\n",
            "Aligning 2 protein sequences with these parameters:\n",
            "        54.94940948\tgap open penalty\n",
            "        8.52492046\tgap extension\n",
            "        4.42409992\tterminal gap penalty\n",
            "        0.20000000\tbonus\n",
            "Alignment will be written to file:'query_out.a3m'.\n",
            "\n",
            "Distance Calculation:\n",
            "     100 percent done\n",
            "Alignment:\n",
            "     100 percent done\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "from Bio import SeqIO\n",
        "\n",
        "msa_sequence = []\n",
        "for record in SeqIO.parse (\"query_out.a3m\", \"fasta\"):\n",
        "  msa_sequence.append(str(record.seq))\n",
        "\n",
        "aa_dict ={}\n",
        "for i, j in enumerate(\"ACDEFGHIKLMNOPQRSTVWY\"):\n",
        "  aa_dict[j]= i\n",
        "  print(aa_dict)\n"
      ],
      "metadata": {
        "id": "OXgH7aKExIRU",
        "outputId": "eee7c35f-0eb5-460f-9840-13dedc406f02",
        "colab": {
          "base_uri": "https://localhost:8080/"
        }
      },
      "execution_count": 13,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "{'A': 0}\n",
            "{'A': 0, 'C': 1}\n",
            "{'A': 0, 'C': 1, 'D': 2}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14, 'R': 15}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14, 'R': 15, 'S': 16}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14, 'R': 15, 'S': 16, 'T': 17}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14, 'R': 15, 'S': 16, 'T': 17, 'V': 18}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14, 'R': 15, 'S': 16, 'T': 17, 'V': 18, 'W': 19}\n",
            "{'A': 0, 'C': 1, 'D': 2, 'E': 3, 'F': 4, 'G': 5, 'H': 6, 'I': 7, 'K': 8, 'L': 9, 'M': 10, 'N': 11, 'O': 12, 'P': 13, 'Q': 14, 'R': 15, 'S': 16, 'T': 17, 'V': 18, 'W': 19, 'Y': 20}\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "import numpy as np \n",
        "\n",
        "def _aatype(sequence):\n",
        "  one_hot = np.eye (21)\n",
        "  results = []\n",
        "  for aa in sequence:\n",
        "    results.append(one_hot[aa_dict[aa]])\n",
        "    return result\n",
        "\n",
        "def _residue_index(sequence):\n",
        "  index_list = np.arange (0,len(sequence)+1)\n",
        "  return index_list\n",
        "\n",
        "  aatype = []\n",
        "  residue_index = []\n",
        "  for sequence in msa_sequence:\n",
        "    aatype.append(_aatype(sequence))\n",
        "    residue_index.append(_residue_index(sequence))\n",
        "\n",
        "aatype = np.asarray(aatype)\n",
        "residue_index = np.asarray(residue_index)\n",
        "\n",
        "feature = {\"aatype\" : aatype, \"residue_index\": residue_index}\n",
        "print(feature)\n"
      ],
      "metadata": {
        "id": "RZkFhRmGzwNT",
        "outputId": "b0f2debc-fe28-4d98-eea1-dc21563f62f3",
        "colab": {
          "base_uri": "https://localhost:8080/",
          "height": 232
        }
      },
      "execution_count": 16,
      "outputs": [
        {
          "output_type": "error",
          "ename": "NameError",
          "evalue": "ignored",
          "traceback": [
            "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
            "\u001b[0;31mNameError\u001b[0m                                 Traceback (most recent call last)",
            "\u001b[0;32m<ipython-input-16-8aa17b883156>\u001b[0m in \u001b[0;36m<cell line: 20>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     18\u001b[0m     \u001b[0mresidue_index\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0m_residue_index\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msequence\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     19\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 20\u001b[0;31m \u001b[0maatype\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0masarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maatype\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     21\u001b[0m \u001b[0mresidue_index\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0masarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mresidue_index\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     22\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
            "\u001b[0;31mNameError\u001b[0m: name 'aatype' is not defined"
          ]
        }
      ]
    }
  ]
}