run_pharokka_and_phold_and_phynteny.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/github/gbouras13/pharokka/blob/master/run_pharokka_and_phold_and_phynteny.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "QGd2GEI3N-02"
      },
      "source": [
        "#Pharokka + Phold + Phynteny\n",
        "\n",
        "[pharokka](https://github.com/gbouras13/pharokka) is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. You can read more about pharokka in the [documentation](https://pharokka.readthedocs.io/).\n",
        "\n",
        "[phold](https://github.com/gbouras13/phold) is a sensitive annotation tool for bacteriophage genomes and metagenomes using protein structural homology. You can read more about phold in the [documentation](https://phold.readthedocs.io/).\n",
        "\n",
        "phold uses the [ProstT5](https://github.com/mheinzinger/ProstT5) protein language model to translate protein amino acid sequences to the 3Di token alphabet used by [Foldseek](https://github.com/steineggerlab/foldseek). Foldseek is then used to search these against a database of 803k protein structures mostly predicted using [Colabfold](https://github.com/sokrypton/ColabFold).\n",
        "\n",
        "[phyntney](https://github.com/susiegriggo/Phynteny) uses a long-short term memory model trained on phage synteny (the conserved gene order across phages) to assign hypothetical phage proteins to a PHROG category.\n",
        "\n",
        "**NOTE: Phynteny will only work if your phage has fewer than 120 predicted genes**\n",
        "\n",
        "**If this is the case for your phage(s), you should just skip running Phynteny (Cells 5+6)**\n",
        "\n",
        "The tools are best run sequentially, as Pharokka conducts extra annotation steps like tRNA, tmRNA, CRISPR and INPHARED searches that Phold lacks (for now at least). Pharokka will also (rarely) annotate CDS that Phold can miss. Phynteny can then help annotate remaining hypothetical proteins with a PHROG category.\n",
        "\n",
        "* **Before you start, please make sure you change the runtime to T4 GPU (or any other kind of GPU if you have $$$), otherwise Phold won't be installed properly**\n",
        "* To do this, go to the top toolbar, then to Runtime -> Change runtime type -> Hardware accelerator\n",
        "\n",
        "* To run the cells, press the play button on the left side\n",
        "* Cells 1 and 2 install pharokka and phold and download the databases/models.\n",
        "* Once they have been run, you can re-run Cell 3 (to run Pharokka), Cell 4 (to run Phold) and Cell 5+6 (to install and run Phynteny) as many times as you would like\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 1,
      "metadata": {
        "id": "Ii39RG8eOZUx",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "d4efb860-d6d4-4f44-b903-f2404361780f"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "python version 3.10\n",
            "installing python\n",
            "installing pharokka and phold\n",
            "Channels:\n",
            " - conda-forge\n",
            " - bioconda\n",
            " - defaults\n",
            "Platform: linux-64\n",
            "Collecting package metadata (repodata.json): ...working... done\n",
            "Solving environment: ...working... done\n",
            "\n",
            "## Package Plan ##\n",
            "\n",
            "  environment location: /usr/local\n",
            "\n",
            "  added / updated specs:\n",
            "    - pharokka==1.7.4\n",
            "    - phold==0.2.0\n",
            "    - pip\n",
            "    - python=3.10\n",
            "    - pytorch[build=cuda*]\n",
            "\n",
            "\n",
            "The following packages will be downloaded:\n",
            "\n",
            "    package                    |            build\n",
            "    ---------------------------|-----------------\n",
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            "    mpfr-4.2.1                 |       h90cbb55_3         620 KB  conda-forge\n",
            "    mpmath-1.3.0               |     pyhd8ed1ab_0         428 KB  conda-forge\n",
            "    multidict-6.1.0            |  py310h89163eb_1          57 KB  conda-forge\n",
            "    multiprocess-0.70.16       |  py310ha75aee5_1         237 KB  conda-forge\n",
            "    munkres-1.1.4              |     pyh9f0ad1d_0          12 KB  conda-forge\n",
            "    mypy_extensions-1.0.0      |     pyha770c72_0          10 KB  conda-forge\n",
            "    nccl-2.23.4.1              |       h2b5d15b_3       118.8 MB  conda-forge\n",
            "    ncurses-6.5                |       he02047a_1         868 KB  conda-forge\n",
            "    networkx-3.4.2             |     pyh267e887_2         1.2 MB  conda-forge\n",
            "    numpy-2.1.3                |  py310hd6e36ab_0         7.5 MB  conda-forge\n",
            "    openjdk-11.0.15            |       hc6918da_0       174.0 MB  conda-forge\n",
            "    openjpeg-2.5.0             |       hfec8fc6_2         344 KB  conda-forge\n",
            "    openssl-3.4.0              |       hb9d3cd8_0         2.8 MB  conda-forge\n",
            "    orc-2.0.1                  |       h17fec99_1        1006 KB  conda-forge\n",
            "    packaging-24.2             |     pyhff2d567_1          59 KB  conda-forge\n",
            "    pandas-2.2.3               |  py310h5eaa309_1        12.4 MB  conda-forge\n",
            "    pathspec-0.12.1            |     pyhd8ed1ab_0          40 KB  conda-forge\n",
            "    patsy-1.0.1                |     pyhff2d567_0         182 KB  conda-forge\n",
            "    perl-5.32.1                | 7_hd590300_perl5        12.7 MB  conda-forge\n",
            "    phanotate-1.5.1            |       h0dbaff4_1          57 KB  bioconda\n",
            "    pharokka-1.7.4             |     pyhdfd78af_0          74 KB  bioconda\n",
            "    phold-0.2.0                |     pyhdfd78af_0        12.4 MB  bioconda\n",
            "    pillow-11.0.0              |  py310hfdbf927_0         814 KB\n",
            "    pip-24.3.1                 |     pyh8b19718_0         1.2 MB  conda-forge\n",
            "    pixman-0.43.2              |       h59595ed_0         378 KB  conda-forge\n",
            "    platformdirs-4.3.6         |     pyhd8ed1ab_0          20 KB  conda-forge\n",
            "    pluggy-1.5.0               |     pyhd8ed1ab_0          23 KB  conda-forge\n",
            "    propcache-0.2.0            |  py310ha75aee5_2          52 KB  conda-forge\n",
            "    psutil-6.1.0               |  py310ha75aee5_0         360 KB  conda-forge\n",
            "    pthread-stubs-0.4          |    hb9d3cd8_1002           8 KB  conda-forge\n",
            "    pyarrow-16.1.0             |  py310hb7f781d_2          28 KB  conda-forge\n",
            "    pyarrow-core-16.1.0        |py310hcccf80d_2_cpu         4.2 MB  conda-forge\n",
            "    pybind11-abi-4             |       hd8ed1ab_3          10 KB  conda-forge\n",
            "    pycirclize-1.7.1           |     pyhd8ed1ab_0          63 KB  conda-forge\n",
            "    pycosat-0.6.6              |  py310ha75aee5_2          83 KB  conda-forge\n",
            "    pyhmmer-0.10.15            |  py310h7c593f9_0         4.5 MB  bioconda\n",
            "    pyparsing-3.2.0            |     pyhd8ed1ab_1          90 KB  conda-forge\n",
            "    pyrodigal-3.6.3            |  py310h7c593f9_0         2.7 MB  bioconda\n",
            "    pyrodigal-gv-0.3.2         |     pyh7e72e81_0         583 KB  bioconda\n",
            "    pysocks-1.7.1              |     pyha2e5f31_6          19 KB  conda-forge\n",
            "    pytest-8.3.3               |     pyhd8ed1ab_0         252 KB  conda-forge\n",
            "    pytest-cov-6.0.0           |     pyhd8ed1ab_0          26 KB  conda-forge\n",
            "    python-3.10.14             |hd12c33a_0_cpython        24.3 MB  conda-forge\n",
            "    python-dateutil-2.9.0.post0|     pyhff2d567_0         217 KB  conda-forge\n",
            "    python-tzdata-2024.2       |     pyhd8ed1ab_0         139 KB  conda-forge\n",
            "    python-xxhash-3.5.0        |  py310ha75aee5_1          22 KB  conda-forge\n",
            "    python_abi-3.10            |          5_cp310           6 KB  conda-forge\n",
            "    pytorch-2.4.0              |cuda120_py310h2c91c31_301        30.6 MB  conda-forge\n",
            "    pytz-2024.1                |     pyhd8ed1ab_0         184 KB  conda-forge\n",
            "    pyyaml-6.0.2               |  py310ha75aee5_1         178 KB  conda-forge\n",
            "    qhull-2020.2               |       h434a139_5         540 KB  conda-forge\n",
            "    re2-2023.09.01             |       h7f4b329_2          26 KB  conda-forge\n",
            "    regex-2024.11.6            |  py310ha75aee5_0         345 KB  conda-forge\n",
            "    requests-2.32.3            |     pyhd8ed1ab_0          57 KB  conda-forge\n",
            "    ruamel.yaml-0.18.6         |  py310ha75aee5_1         198 KB  conda-forge\n",
            "    ruamel.yaml.clib-0.2.8     |  py310ha75aee5_1         143 KB  conda-forge\n",
            "    s2n-1.4.15                 |       he19d79f_0         341 KB  conda-forge\n",
            "    safetensors-0.4.5          |  py310h505e2c1_0         388 KB  conda-forge\n",
            "    scipy-1.14.1               |  py310hfcf56fc_1        16.1 MB  conda-forge\n",
            "    seaborn-0.13.2             |       hd8ed1ab_2           7 KB  conda-forge\n",
            "    seaborn-base-0.13.2        |     pyhd8ed1ab_2         229 KB  conda-forge\n",
            "    sentencepiece-0.2.0        |       hff52083_4          17 KB  conda-forge\n",
            "    sentencepiece-python-0.2.0 |  py310hcf7cfdd_4         2.3 MB  conda-forge\n",
            "    sentencepiece-spm-0.2.0    |       hc656cff_4          84 KB  conda-forge\n",
            "    setuptools-75.6.0          |     pyhff2d567_1         756 KB  conda-forge\n",
            "    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge\n",
            "    sleef-3.7                  |       h1b44611_2         1.8 MB  conda-forge\n",
            "    snappy-1.2.1               |       ha2e4443_0          41 KB  conda-forge\n",
            "    statsmodels-0.14.4         |  py310hf462985_0        10.4 MB  conda-forge\n",
            "    sympy-1.13.3               | pypyh2585a3b_103         4.4 MB  conda-forge\n",
            "    tbb-2021.13.0              |       h84d6215_0         172 KB  conda-forge\n",
            "    textwrap3-0.9.2            |             py_0          12 KB  conda-forge\n",
            "    tokenizers-0.20.4          |  py310hb1c6e2c_0         2.1 MB  conda-forge\n",
            "    toml-0.10.2                |     pyhd8ed1ab_0          18 KB  conda-forge\n",
            "    tomli-2.1.0                |     pyhff2d567_0          18 KB  conda-forge\n",
            "    tqdm-4.67.1                |     pyhd8ed1ab_0          87 KB  conda-forge\n",
            "    transformers-4.46.3        |     pyhd8ed1ab_0         3.5 MB  conda-forge\n",
            "    trnascan-se-2.0.12         | pl5321h031d066_1         3.1 MB  bioconda\n",
            "    truststore-0.10.0          |     pyhd8ed1ab_0          21 KB  conda-forge\n",
            "    typing-extensions-4.12.2   |       hd8ed1ab_0          10 KB  conda-forge\n",
            "    typing_extensions-4.12.2   |     pyha770c72_0          39 KB  conda-forge\n",
            "    unicodedata2-15.1.0        |  py310ha75aee5_1         359 KB  conda-forge\n",
            "    urllib3-2.2.3              |     pyhd8ed1ab_0          96 KB  conda-forge\n",
            "    wget-1.21.4                |       hda4d442_0         752 KB  conda-forge\n",
            "    wheel-0.45.1               |     pyhd8ed1ab_0          62 KB  conda-forge\n",
            "    xorg-libx11-1.8.10         |       h4f16b4b_0         819 KB  conda-forge\n",
            "    xorg-libxau-1.0.11         |       hb9d3cd8_1          14 KB  conda-forge\n",
            "    xorg-libxdmcp-1.1.5        |       hb9d3cd8_0          19 KB  conda-forge\n",
            "    xorg-libxext-1.3.6         |       hb9d3cd8_0          49 KB  conda-forge\n",
            "    xorg-libxfixes-6.0.1       |       hb9d3cd8_0          19 KB  conda-forge\n",
            "    xorg-libxi-1.8.2           |       hb9d3cd8_0          46 KB  conda-forge\n",
            "    xorg-libxrender-0.9.11     |       hb9d3cd8_1          37 KB  conda-forge\n",
            "    xorg-libxtst-1.2.5         |       hb9d3cd8_3          32 KB  conda-forge\n",
            "    xorg-xorgproto-2024.1      |       hb9d3cd8_1         552 KB  conda-forge\n",
            "    xxhash-0.8.2               |       hd590300_0          95 KB  conda-forge\n",
            "    yaml-0.2.5                 |       h7f98852_2          87 KB  conda-forge\n",
            "    yarl-1.18.0                |  py310ha75aee5_0         136 KB  conda-forge\n",
            "    zlib-1.2.13                |       h4ab18f5_6          91 KB  conda-forge\n",
            "    zstandard-0.23.0           |  py310ha39cb0e_1         399 KB  conda-forge\n",
            "    ------------------------------------------------------------\n",
            "                                           Total:        2.58 GB\n",
            "\n",
            "The following NEW packages will be INSTALLED:\n",
            "\n",
            "  about-time         conda-forge/noarch::about-time-4.2.1-pyhd8ed1ab_0 \n",
            "  aiohappyeyeballs   conda-forge/noarch::aiohappyeyeballs-2.4.3-pyhd8ed1ab_0 \n",
            "  aiohttp            conda-forge/linux-64::aiohttp-3.11.7-py310h89163eb_0 \n",
            "  aiosignal          conda-forge/noarch::aiosignal-1.3.1-pyhd8ed1ab_0 \n",
            "  alive-progress     conda-forge/noarch::alive-progress-3.1.5-pyhd8ed1ab_0 \n",
            "  alsa-lib           conda-forge/linux-64::alsa-lib-1.2.6.1-h7f98852_0 \n",
            "  aragorn            bioconda/linux-64::aragorn-1.2.41-h031d066_3 \n",
            "  aria2              conda-forge/linux-64::aria2-1.37.0-h347180d_1 \n",
            "  async-timeout      conda-forge/noarch::async-timeout-5.0.1-pyhd8ed1ab_0 \n",
            "  attrs              conda-forge/noarch::attrs-24.2.0-pyh71513ae_0 \n",
            "  aws-c-auth         conda-forge/linux-64::aws-c-auth-0.7.22-h96bc93b_2 \n",
            "  aws-c-cal          conda-forge/linux-64::aws-c-cal-0.6.14-h88a6e22_1 \n",
            "  aws-c-common       conda-forge/linux-64::aws-c-common-0.9.19-h4ab18f5_0 \n",
            "  aws-c-compression  conda-forge/linux-64::aws-c-compression-0.2.18-h83b837d_6 \n",
            "  aws-c-event-stream conda-forge/linux-64::aws-c-event-stream-0.4.2-ha47c788_12 \n",
            "  aws-c-http         conda-forge/linux-64::aws-c-http-0.8.1-h29d6fba_17 \n",
            "  aws-c-io           conda-forge/linux-64::aws-c-io-0.14.8-h21d4f22_5 \n",
            "  aws-c-mqtt         conda-forge/linux-64::aws-c-mqtt-0.10.4-h759edc4_4 \n",
            "  aws-c-s3           conda-forge/linux-64::aws-c-s3-0.5.9-h594631b_3 \n",
            "  aws-c-sdkutils     conda-forge/linux-64::aws-c-sdkutils-0.1.16-h83b837d_2 \n",
            "  aws-checksums      conda-forge/linux-64::aws-checksums-0.1.18-h83b837d_6 \n",
            "  aws-crt-cpp        conda-forge/linux-64::aws-crt-cpp-0.26.9-he3a8b3b_0 \n",
            "  aws-sdk-cpp        conda-forge/linux-64::aws-sdk-cpp-1.11.329-hba8bd5f_3 \n",
            "  backports          conda-forge/noarch::backports-1.0-pyhd8ed1ab_4 \n",
            "  backports.tempfile conda-forge/noarch::backports.tempfile-1.0-py_0 \n",
            "  backports.weakref  conda-forge/noarch::backports.weakref-1.0.post1-pyhd8ed1ab_1003 \n",
            "  bcbio-gff          bioconda/noarch::bcbio-gff-0.7.1-pyh7e72e81_2 \n",
            "  biopython          conda-forge/linux-64::biopython-1.81-py310h2372a71_1 \n",
            "  black              conda-forge/linux-64::black-24.10.0-py310hff52083_0 \n",
            "  brotli             conda-forge/linux-64::brotli-1.1.0-hb9d3cd8_2 \n",
            "  brotli-bin         conda-forge/linux-64::brotli-bin-1.1.0-hb9d3cd8_2 \n",
            "  bx-python          bioconda/linux-64::bx-python-0.13.0-py310ha025fb0_0 \n",
            "  cached-property    conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 \n",
            "  cached_property    conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 \n",
            "  cairo              pkgs/main/linux-64::cairo-1.16.0-hb05425b_5 \n",
            "  capnproto          conda-forge/linux-64::capnproto-1.0.2-h2b92303_1 \n",
            "  click              conda-forge/noarch::click-8.1.7-unix_pyh707e725_0 \n",
            "  colorama           conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 \n",
            "  contourpy          conda-forge/linux-64::contourpy-1.3.1-py310h3788b33_0 \n",
            "  coverage           conda-forge/linux-64::coverage-7.6.8-py310h89163eb_0 \n",
            "  cuda-cudart        conda-forge/linux-64::cuda-cudart-12.6.77-h5888daf_0 \n",
            "  cuda-cudart_linux~ conda-forge/noarch::cuda-cudart_linux-64-12.6.77-h3f2d84a_0 \n",
            "  cuda-nvrtc         conda-forge/linux-64::cuda-nvrtc-12.6.85-hbd13f7d_0 \n",
            "  cuda-nvtx          conda-forge/linux-64::cuda-nvtx-12.6.77-hbd13f7d_0 \n",
            "  cuda-version       conda-forge/noarch::cuda-version-12.6-h7480c83_3 \n",
            "  cudnn              conda-forge/linux-64::cudnn-8.9.7.29-h092f7fd_3 \n",
            "  cycler             conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0 \n",
            "  datasets           conda-forge/noarch::datasets-3.1.0-pyhff2d567_0 \n",
            "  dill               conda-forge/noarch::dill-0.3.8-pyhd8ed1ab_0 \n",
            "  dnaapler           bioconda/noarch::dnaapler-1.0.1-pyhdfd78af_0 \n",
            "  exceptiongroup     conda-forge/noarch::exceptiongroup-1.2.2-pyhd8ed1ab_0 \n",
            "  fastpath           conda-forge/linux-64::fastpath-1.9-py310h2372a71_3 \n",
            "  filelock           conda-forge/noarch::filelock-3.16.1-pyhd8ed1ab_0 \n",
            "  foldseek           bioconda/linux-64::foldseek-9.427df8a-pl5321hb365157_1 \n",
            "  font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 \n",
            "  font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0 \n",
            "  font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0 \n",
            "  font-ttf-ubuntu    conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_3 \n",
            "  fontconfig         conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0 \n",
            "  fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0 \n",
            "  fonts-conda-forge  conda-forge/noarch::fonts-conda-forge-1-0 \n",
            "  fonttools          conda-forge/linux-64::fonttools-4.55.0-py310h89163eb_0 \n",
            "  freetype           conda-forge/linux-64::freetype-2.12.1-h267a509_2 \n",
            "  frozenlist         conda-forge/linux-64::frozenlist-1.5.0-py310ha75aee5_0 \n",
            "  fsspec             conda-forge/noarch::fsspec-2024.9.0-pyhff2d567_0 \n",
            "  gawk               conda-forge/linux-64::gawk-5.3.1-hcd3d067_0 \n",
            "  gettext            conda-forge/linux-64::gettext-0.22.5-he02047a_3 \n",
            "  gettext-tools      conda-forge/linux-64::gettext-tools-0.22.5-he02047a_3 \n",
            "  gflags             conda-forge/linux-64::gflags-2.2.2-h5888daf_1005 \n",
            "  giflib             conda-forge/linux-64::giflib-5.2.2-hd590300_0 \n",
            "  glib               conda-forge/linux-64::glib-2.78.4-hfc55251_0 \n",
            "  glib-tools         conda-forge/linux-64::glib-tools-2.78.4-hfc55251_0 \n",
            "  glog               conda-forge/linux-64::glog-0.7.1-hbabe93e_0 \n",
            "  gmp                conda-forge/linux-64::gmp-6.3.0-hac33072_2 \n",
            "  gmpy2              conda-forge/linux-64::gmpy2-2.1.5-py310he8512ff_2 \n",
            "  grapheme           conda-forge/noarch::grapheme-0.6.0-pyhd8ed1ab_0 \n",
            "  graphite2          pkgs/main/linux-64::graphite2-1.3.14-h295c915_1 \n",
            "  gsl                conda-forge/linux-64::gsl-2.7-he838d99_0 \n",
            "  h2                 conda-forge/noarch::h2-4.1.0-pyhd8ed1ab_0 \n",
            "  h5py               conda-forge/linux-64::h5py-3.12.1-nompi_py310h60e0fe6_102 \n",
            "  harfbuzz           pkgs/main/linux-64::harfbuzz-4.3.0-hf52aaf7_2 \n",
            "  hdf5               conda-forge/linux-64::hdf5-1.14.3-nompi_hdf9ad27_105 \n",
            "  hpack              conda-forge/noarch::hpack-4.0.0-pyh9f0ad1d_0 \n",
            "  huggingface_hub    conda-forge/noarch::huggingface_hub-0.26.2-pyh0610db2_0 \n",
            "  hyperframe         conda-forge/noarch::hyperframe-6.0.1-pyhd8ed1ab_0 \n",
            "  infernal           bioconda/linux-64::infernal-1.1.5-pl5321h031d066_3 \n",
            "  iniconfig          conda-forge/noarch::iniconfig-2.0.0-pyhd8ed1ab_0 \n",
            "  isort              conda-forge/noarch::isort-5.13.2-pyhd8ed1ab_0 \n",
            "  jinja2             conda-forge/noarch::jinja2-3.1.4-pyhd8ed1ab_0 \n",
            "  jpeg               conda-forge/linux-64::jpeg-9e-h0b41bf4_3 \n",
            "  kiwisolver         conda-forge/linux-64::kiwisolver-1.4.7-py310h3788b33_0 \n",
            "  lcms2              conda-forge/linux-64::lcms2-2.15-hfd0df8a_0 \n",
            "  lerc               conda-forge/linux-64::lerc-4.0.0-h27087fc_0 \n",
            "  libabseil          conda-forge/linux-64::libabseil-20240116.2-cxx17_he02047a_1 \n",
            "  libaec             conda-forge/linux-64::libaec-1.1.3-h59595ed_0 \n",
            "  libarrow           conda-forge/linux-64::libarrow-16.1.0-hcb6531f_6_cpu \n",
            "  libarrow-acero     conda-forge/linux-64::libarrow-acero-16.1.0-hac33072_6_cpu \n",
            "  libarrow-dataset   conda-forge/linux-64::libarrow-dataset-16.1.0-hac33072_6_cpu \n",
            "  libarrow-substrait conda-forge/linux-64::libarrow-substrait-16.1.0-h7e0c224_6_cpu \n",
            "  libasprintf        conda-forge/linux-64::libasprintf-0.22.5-he8f35ee_3 \n",
            "  libasprintf-devel  conda-forge/linux-64::libasprintf-devel-0.22.5-he8f35ee_3 \n",
            "  libblas            conda-forge/linux-64::libblas-3.9.0-25_linux64_openblas \n",
            "  libbrotlicommon    conda-forge/linux-64::libbrotlicommon-1.1.0-hb9d3cd8_2 \n",
            "  libbrotlidec       conda-forge/linux-64::libbrotlidec-1.1.0-hb9d3cd8_2 \n",
            "  libbrotlienc       conda-forge/linux-64::libbrotlienc-1.1.0-hb9d3cd8_2 \n",
            "  libcblas           conda-forge/linux-64::libcblas-3.9.0-25_linux64_openblas \n",
            "  libcrc32c          conda-forge/linux-64::libcrc32c-1.1.2-h9c3ff4c_0 \n",
            "  libcublas          conda-forge/linux-64::libcublas-12.6.4.1-hbd13f7d_0 \n",
            "  libcufft           conda-forge/linux-64::libcufft-11.3.0.4-hbd13f7d_0 \n",
            "  libcups            conda-forge/linux-64::libcups-2.3.3-h36d4200_3 \n",
            "  libcurand          conda-forge/linux-64::libcurand-10.3.7.77-hbd13f7d_0 \n",
            "  libcusolver        conda-forge/linux-64::libcusolver-11.7.1.2-hbd13f7d_0 \n",
            "  libcusparse        conda-forge/linux-64::libcusparse-12.5.4.2-hbd13f7d_0 \n",
            "  libdeflate         conda-forge/linux-64::libdeflate-1.17-h0b41bf4_0 \n",
            "  libevent           conda-forge/linux-64::libevent-2.1.12-hf998b51_1 \n",
            "  libgcc             conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 \n",
            "  libgettextpo       conda-forge/linux-64::libgettextpo-0.22.5-he02047a_3 \n",
            "  libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.22.5-he02047a_3 \n",
            "  libgfortran        conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1 \n",
            "  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1 \n",
            "  libgfortran5       conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1 \n",
            "  libglib            conda-forge/linux-64::libglib-2.78.4-h783c2da_0 \n",
            "  libgoogle-cloud    conda-forge/linux-64::libgoogle-cloud-2.24.0-h2736e30_0 \n",
            "  libgoogle-cloud-s~ conda-forge/linux-64::libgoogle-cloud-storage-2.24.0-h3d9a0c8_0 \n",
            "  libgrpc            conda-forge/linux-64::libgrpc-1.62.2-h15f2491_0 \n",
            "  libhwloc           conda-forge/linux-64::libhwloc-2.11.1-default_hecaa2ac_1000 \n",
            "  libiconv           conda-forge/linux-64::libiconv-1.17-hd590300_2 \n",
            "  libidn2            conda-forge/linux-64::libidn2-2.3.7-hd590300_0 \n",
            "  liblapack          conda-forge/linux-64::liblapack-3.9.0-25_linux64_openblas \n",
            "  libmagma           conda-forge/linux-64::libmagma-2.8.0-h0af6554_0 \n",
            "  libmagma_sparse    conda-forge/linux-64::libmagma_sparse-2.8.0-h0af6554_0 \n",
            "  libnsl             conda-forge/linux-64::libnsl-2.0.1-hd590300_0 \n",
            "  libnvjitlink       conda-forge/linux-64::libnvjitlink-12.6.85-hbd13f7d_0 \n",
            "  libopenblas        conda-forge/linux-64::libopenblas-0.3.28-pthreads_h94d23a6_1 \n",
            "  libparquet         conda-forge/linux-64::libparquet-16.1.0-h6a7eafb_6_cpu \n",
            "  libpng             conda-forge/linux-64::libpng-1.6.43-h2797004_0 \n",
            "  libprotobuf        conda-forge/linux-64::libprotobuf-4.25.3-h08a7969_0 \n",
            "  libre2-11          conda-forge/linux-64::libre2-11-2023.09.01-h5a48ba9_2 \n",
            "  libsentencepiece   conda-forge/linux-64::libsentencepiece-0.2.0-hc656cff_4 \n",
            "  libsqlite          conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 \n",
            "  libstdcxx          conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1 \n",
            "  libthrift          conda-forge/linux-64::libthrift-0.19.0-hb90f79a_1 \n",
            "  libtiff            conda-forge/linux-64::libtiff-4.5.0-h6adf6a1_2 \n",
            "  libtorch           conda-forge/linux-64::libtorch-2.4.0-cuda120_h2b0da52_301 \n",
            "  libunistring       conda-forge/linux-64::libunistring-0.9.10-h7f98852_0 \n",
            "  libutf8proc        conda-forge/linux-64::libutf8proc-2.8.0-h166bdaf_0 \n",
            "  libuv              conda-forge/linux-64::libuv-1.49.2-hb9d3cd8_0 \n",
            "  libwebp-base       conda-forge/linux-64::libwebp-base-1.4.0-hd590300_0 \n",
            "  libxcb             conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 \n",
            "  libxcrypt          conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 \n",
            "  libzlib            conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6 \n",
            "  llvm-openmp        conda-forge/linux-64::llvm-openmp-19.1.4-h024ca30_0 \n",
            "  loguru             conda-forge/linux-64::loguru-0.7.2-py310hff52083_2 \n",
            "  markupsafe         conda-forge/linux-64::markupsafe-3.0.2-py310h89163eb_0 \n",
            "  mash               bioconda/linux-64::mash-2.3-hc74b729_7 \n",
            "  matplotlib-base    conda-forge/linux-64::matplotlib-base-3.9.2-py310h68603db_2 \n",
            "  minced             bioconda/noarch::minced-0.4.2-hdfd78af_1 \n",
            "  mkl                conda-forge/linux-64::mkl-2023.2.0-h84fe81f_50496 \n",
            "  mmseqs2            bioconda/linux-64::mmseqs2-13.45111-pl5321hf1761c0_2 \n",
            "  mpc                conda-forge/linux-64::mpc-1.3.1-h24ddda3_1 \n",
            "  mpfr               conda-forge/linux-64::mpfr-4.2.1-h90cbb55_3 \n",
            "  mpmath             conda-forge/noarch::mpmath-1.3.0-pyhd8ed1ab_0 \n",
            "  multidict          conda-forge/linux-64::multidict-6.1.0-py310h89163eb_1 \n",
            "  multiprocess       conda-forge/linux-64::multiprocess-0.70.16-py310ha75aee5_1 \n",
            "  munkres            conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0 \n",
            "  mypy_extensions    conda-forge/noarch::mypy_extensions-1.0.0-pyha770c72_0 \n",
            "  nccl               conda-forge/linux-64::nccl-2.23.4.1-h2b5d15b_3 \n",
            "  networkx           conda-forge/noarch::networkx-3.4.2-pyh267e887_2 \n",
            "  numpy              conda-forge/linux-64::numpy-2.1.3-py310hd6e36ab_0 \n",
            "  openjdk            conda-forge/linux-64::openjdk-11.0.15-hc6918da_0 \n",
            "  openjpeg           conda-forge/linux-64::openjpeg-2.5.0-hfec8fc6_2 \n",
            "  orc                conda-forge/linux-64::orc-2.0.1-h17fec99_1 \n",
            "  pandas             conda-forge/linux-64::pandas-2.2.3-py310h5eaa309_1 \n",
            "  pathspec           conda-forge/noarch::pathspec-0.12.1-pyhd8ed1ab_0 \n",
            "  patsy              conda-forge/noarch::patsy-1.0.1-pyhff2d567_0 \n",
            "  perl               conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5 \n",
            "  phanotate          bioconda/linux-64::phanotate-1.5.1-h0dbaff4_1 \n",
            "  pharokka           bioconda/noarch::pharokka-1.7.4-pyhdfd78af_0 \n",
            "  phold              bioconda/noarch::phold-0.2.0-pyhdfd78af_0 \n",
            "  pillow             pkgs/main/linux-64::pillow-11.0.0-py310hfdbf927_0 \n",
            "  pixman             conda-forge/linux-64::pixman-0.43.2-h59595ed_0 \n",
            "  propcache          conda-forge/linux-64::propcache-0.2.0-py310ha75aee5_2 \n",
            "  psutil             conda-forge/linux-64::psutil-6.1.0-py310ha75aee5_0 \n",
            "  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 \n",
            "  pyarrow            conda-forge/linux-64::pyarrow-16.1.0-py310hb7f781d_2 \n",
            "  pyarrow-core       conda-forge/linux-64::pyarrow-core-16.1.0-py310hcccf80d_2_cpu \n",
            "  pycirclize         conda-forge/noarch::pycirclize-1.7.1-pyhd8ed1ab_0 \n",
            "  pyhmmer            bioconda/linux-64::pyhmmer-0.10.15-py310h7c593f9_0 \n",
            "  pyparsing          conda-forge/noarch::pyparsing-3.2.0-pyhd8ed1ab_1 \n",
            "  pyrodigal          bioconda/linux-64::pyrodigal-3.6.3-py310h7c593f9_0 \n",
            "  pyrodigal-gv       bioconda/noarch::pyrodigal-gv-0.3.2-pyh7e72e81_0 \n",
            "  pytest             conda-forge/noarch::pytest-8.3.3-pyhd8ed1ab_0 \n",
            "  pytest-cov         conda-forge/noarch::pytest-cov-6.0.0-pyhd8ed1ab_0 \n",
            "  python-dateutil    conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_0 \n",
            "  python-tzdata      conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0 \n",
            "  python-xxhash      conda-forge/linux-64::python-xxhash-3.5.0-py310ha75aee5_1 \n",
            "  python_abi         conda-forge/linux-64::python_abi-3.10-5_cp310 \n",
            "  pytorch            conda-forge/linux-64::pytorch-2.4.0-cuda120_py310h2c91c31_301 \n",
            "  pytz               conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 \n",
            "  pyyaml             conda-forge/linux-64::pyyaml-6.0.2-py310ha75aee5_1 \n",
            "  qhull              conda-forge/linux-64::qhull-2020.2-h434a139_5 \n",
            "  re2                conda-forge/linux-64::re2-2023.09.01-h7f4b329_2 \n",
            "  regex              conda-forge/linux-64::regex-2024.11.6-py310ha75aee5_0 \n",
            "  s2n                conda-forge/linux-64::s2n-1.4.15-he19d79f_0 \n",
            "  safetensors        conda-forge/linux-64::safetensors-0.4.5-py310h505e2c1_0 \n",
            "  scipy              conda-forge/linux-64::scipy-1.14.1-py310hfcf56fc_1 \n",
            "  seaborn            conda-forge/noarch::seaborn-0.13.2-hd8ed1ab_2 \n",
            "  seaborn-base       conda-forge/noarch::seaborn-base-0.13.2-pyhd8ed1ab_2 \n",
            "  sentencepiece      conda-forge/linux-64::sentencepiece-0.2.0-hff52083_4 \n",
            "  sentencepiece-pyt~ conda-forge/linux-64::sentencepiece-python-0.2.0-py310hcf7cfdd_4 \n",
            "  sentencepiece-spm  conda-forge/linux-64::sentencepiece-spm-0.2.0-hc656cff_4 \n",
            "  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 \n",
            "  sleef              conda-forge/linux-64::sleef-3.7-h1b44611_2 \n",
            "  snappy             conda-forge/linux-64::snappy-1.2.1-ha2e4443_0 \n",
            "  statsmodels        conda-forge/linux-64::statsmodels-0.14.4-py310hf462985_0 \n",
            "  sympy              conda-forge/noarch::sympy-1.13.3-pypyh2585a3b_103 \n",
            "  tbb                conda-forge/linux-64::tbb-2021.13.0-h84d6215_0 \n",
            "  textwrap3          conda-forge/noarch::textwrap3-0.9.2-py_0 \n",
            "  tokenizers         conda-forge/linux-64::tokenizers-0.20.4-py310hb1c6e2c_0 \n",
            "  toml               conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0 \n",
            "  tomli              conda-forge/noarch::tomli-2.1.0-pyhff2d567_0 \n",
            "  transformers       conda-forge/noarch::transformers-4.46.3-pyhd8ed1ab_0 \n",
            "  trnascan-se        bioconda/linux-64::trnascan-se-2.0.12-pl5321h031d066_1 \n",
            "  typing-extensions  conda-forge/noarch::typing-extensions-4.12.2-hd8ed1ab_0 \n",
            "  typing_extensions  conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_0 \n",
            "  unicodedata2       conda-forge/linux-64::unicodedata2-15.1.0-py310ha75aee5_1 \n",
            "  wget               conda-forge/linux-64::wget-1.21.4-hda4d442_0 \n",
            "  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.10-h4f16b4b_0 \n",
            "  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.11-hb9d3cd8_1 \n",
            "  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0 \n",
            "  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 \n",
            "  xorg-libxfixes     conda-forge/linux-64::xorg-libxfixes-6.0.1-hb9d3cd8_0 \n",
            "  xorg-libxi         conda-forge/linux-64::xorg-libxi-1.8.2-hb9d3cd8_0 \n",
            "  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.11-hb9d3cd8_1 \n",
            "  xorg-libxtst       conda-forge/linux-64::xorg-libxtst-1.2.5-hb9d3cd8_3 \n",
            "  xorg-xorgproto     conda-forge/linux-64::xorg-xorgproto-2024.1-hb9d3cd8_1 \n",
            "  xxhash             conda-forge/linux-64::xxhash-0.8.2-hd590300_0 \n",
            "  yaml               conda-forge/linux-64::yaml-0.2.5-h7f98852_2 \n",
            "  yarl               conda-forge/linux-64::yarl-1.18.0-py310ha75aee5_0 \n",
            "\n",
            "The following packages will be UPDATED:\n",
            "\n",
            "  anaconda-anon-usa~                0.4.4-py312hfc0e8ea_100 --> 0.5.0-py310hfc0e8ea_100 \n",
            "  boltons            pkgs/main/linux-64::boltons-23.0.0-py~ --> conda-forge/noarch::boltons-24.0.0-pyhd8ed1ab_0 \n",
            "  brotli-python      pkgs/main::brotli-python-1.0.9-py312h~ --> conda-forge::brotli-python-1.1.0-py310hf71b8c6_2 \n",
            "  c-ares                pkgs/main::c-ares-1.19.1-h5eee18b_0 --> conda-forge::c-ares-1.34.3-hb9d3cd8_1 \n",
            "  conda-package-han~ pkgs/main/linux-64::conda-package-han~ --> conda-forge/noarch::conda-package-handling-2.4.0-pyh7900ff3_0 \n",
            "  conda-package-str~ pkgs/main/linux-64::conda-package-str~ --> conda-forge/noarch::conda-package-streaming-0.11.0-pyhd8ed1ab_0 \n",
            "  cryptography       pkgs/main::cryptography-43.0.0-py312h~ --> conda-forge::cryptography-44.0.0-py310h6c63255_0 \n",
            "  frozendict         pkgs/main::frozendict-2.4.2-py312h06a~ --> conda-forge::frozendict-2.4.6-py310ha75aee5_0 \n",
            "  idna               pkgs/main/linux-64::idna-3.7-py312h06~ --> conda-forge/noarch::idna-3.10-pyhd8ed1ab_0 \n",
            "  libgcc-ng          pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-14.2.0-h69a702a_1 \n",
            "  libgomp              pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-14.2.0-h77fa898_1 \n",
            "  libstdcxx-ng       pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-14.2.0-h4852527_1 \n",
            "  libuuid              pkgs/main::libuuid-1.41.5-h5eee18b_0 --> conda-forge::libuuid-2.38.1-h0b41bf4_0 \n",
            "  menuinst           pkgs/main::menuinst-2.1.2-py312h06a43~ --> conda-forge::menuinst-2.2.0-py310hff52083_0 \n",
            "  ncurses                 pkgs/main::ncurses-6.4-h6a678d5_0 --> conda-forge::ncurses-6.5-he02047a_1 \n",
            "  openssl              pkgs/main::openssl-3.0.15-h5eee18b_0 --> conda-forge::openssl-3.4.0-hb9d3cd8_0 \n",
            "  packaging          pkgs/main/linux-64::packaging-24.1-py~ --> conda-forge/noarch::packaging-24.2-pyhff2d567_1 \n",
            "  pip                pkgs/main/linux-64::pip-24.2-py312h06~ --> conda-forge/noarch::pip-24.3.1-pyh8b19718_0 \n",
            "  platformdirs       pkgs/main/linux-64::platformdirs-3.10~ --> conda-forge/noarch::platformdirs-4.3.6-pyhd8ed1ab_0 \n",
            "  pluggy             pkgs/main/linux-64::pluggy-1.0.0-py31~ --> conda-forge/noarch::pluggy-1.5.0-pyhd8ed1ab_0 \n",
            "  pycosat            pkgs/main::pycosat-0.6.6-py312h5eee18~ --> conda-forge::pycosat-0.6.6-py310ha75aee5_2 \n",
            "  pysocks            pkgs/main/linux-64::pysocks-1.7.1-py3~ --> conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6 \n",
            "  ruamel.yaml        pkgs/main::ruamel.yaml-0.18.6-py312h5~ --> conda-forge::ruamel.yaml-0.18.6-py310ha75aee5_1 \n",
            "  ruamel.yaml.clib   pkgs/main::ruamel.yaml.clib-0.2.8-py3~ --> conda-forge::ruamel.yaml.clib-0.2.8-py310ha75aee5_1 \n",
            "  setuptools         pkgs/main/linux-64::setuptools-75.1.0~ --> conda-forge/noarch::setuptools-75.6.0-pyhff2d567_1 \n",
            "  tqdm               pkgs/main/linux-64::tqdm-4.66.5-py312~ --> conda-forge/noarch::tqdm-4.67.1-pyhd8ed1ab_0 \n",
            "  truststore         pkgs/main/linux-64::truststore-0.8.0-~ --> conda-forge/noarch::truststore-0.10.0-pyhd8ed1ab_0 \n",
            "  wheel              pkgs/main/linux-64::wheel-0.44.0-py31~ --> conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_0 \n",
            "  zlib                    pkgs/main::zlib-1.2.13-h5eee18b_1 --> conda-forge::zlib-1.2.13-h4ab18f5_6 \n",
            "  zstandard          pkgs/main::zstandard-0.23.0-py312h2c3~ --> conda-forge::zstandard-0.23.0-py310ha39cb0e_1 \n",
            "\n",
            "The following packages will be SUPERSEDED by a higher-priority channel:\n",
            "\n",
            "  _libgcc_mutex           pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge \n",
            "  _openmp_mutex          pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_kmp_llvm \n",
            "  certifi            pkgs/main/linux-64::certifi-2024.8.30~ --> conda-forge/noarch::certifi-2024.8.30-pyhd8ed1ab_0 \n",
            "  cffi               pkgs/main::cffi-1.17.1-py312h1fdaa30_0 --> conda-forge::cffi-1.17.1-py310h8deb56e_0 \n",
            "  conda              pkgs/main::conda-24.9.2-py312h06a4308~ --> conda-forge::conda-24.9.2-py310hff52083_0 \n",
            "  conda-content-tru~ pkgs/main/linux-64::conda-content-tru~ --> conda-forge/noarch::conda-content-trust-0.2.0-pyhd8ed1ab_0 \n",
            "  distro             pkgs/main/linux-64::distro-1.9.0-py31~ --> conda-forge/noarch::distro-1.9.0-pyhd8ed1ab_0 \n",
            "  jsonpatch          pkgs/main/linux-64::jsonpatch-1.33-py~ --> conda-forge/noarch::jsonpatch-1.33-pyhd8ed1ab_0 \n",
            "  pybind11-abi         pkgs/main::pybind11-abi-5-hd3eb1b0_0 --> conda-forge::pybind11-abi-4-hd8ed1ab_3 \n",
            "  python                pkgs/main::python-3.12.7-h5148396_0 --> conda-forge::python-3.10.14-hd12c33a_0_cpython \n",
            "  requests           pkgs/main/linux-64::requests-2.32.3-p~ --> conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_0 \n",
            "  urllib3            pkgs/main/linux-64::urllib3-2.2.3-py3~ --> conda-forge/noarch::urllib3-2.2.3-pyhd8ed1ab_0 \n",
            "\n",
            "The following packages will be DOWNGRADED:\n",
            "\n",
            "  libmambapy                          1.5.8-py312h2dafd23_3 --> 1.5.8-py310h2dafd23_3 \n",
            "\n",
            "\n",
            "\n",
            "Downloading and Extracting Packages: ...working... done\n",
            "Preparing transaction: ...working... done\n",
            "Verifying transaction: ...working... done\n",
            "Executing transaction: ...working... By downloading and using the cuDNN conda packages, you accept the terms and conditions of the NVIDIA cuDNN EULA -\n",
            "  https://docs.nvidia.com/deeplearning/cudnn/sla/index.html\n",
            "\n",
            "done\n"
          ]
        }
      ],
      "source": [
        "#@title 1. Install pharokka and phold\n",
        "\n",
        "#@markdown This cell installs pharokka and phold. It will take a few minutes. Please be patient\n",
        "\n",
        "%%bash\n",
        "\n",
        "set -e\n",
        "\n",
        "PYTHON_VERSION=\"3.10\"\n",
        "PHAROKKA_VERSION=\"1.7.4\"\n",
        "PHOLD_VERSION=\"0.2.0\"\n",
        "\n",
        "echo \"python version ${PYTHON_VERSION}\"\n",
        "\n",
        "if [ ! -f CONDA_READY ]; then\n",
        "  echo \"installing python\"\n",
        "  wget -qnc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh\n",
        "  bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local 2>&1 1>/dev/null\n",
        "  rm Miniconda3-latest-Linux-x86_64.sh\n",
        "  conda config --set auto_update_conda false\n",
        "  touch CONDA_READY\n",
        "fi\n",
        "\n",
        "if [ ! -f PHAROKKA_PHOLD_READY ]; then\n",
        "  echo \"installing pharokka and phold\"\n",
        "  conda install -y -c conda-forge -c bioconda pip pharokka==${PHAROKKA_VERSION} python=${PYTHON_VERSION} phold==${PHOLD_VERSION} pytorch=*=cuda*\n",
        "  touch PHAROKKA_PHOLD_READY\n",
        "fi\n",
        "\n",
        "\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 2,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "tfltpbZ_QLfZ",
        "outputId": "d5de66ae-7a1b-44f6-bb67-e10beda22c75"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Downloading pharokka database. This will take a few minutes. Please be patient :)\n",
            "Downloading phold database. This will take a few minutes. Please be patient :)\n",
            "CPU times: user 1.22 s, sys: 188 ms, total: 1.41 s\n",
            "Wall time: 6min 4s\n"
          ]
        },
        {
          "output_type": "execute_result",
          "data": {
            "text/plain": [
              "0"
            ]
          },
          "metadata": {},
          "execution_count": 2
        }
      ],
      "source": [
        "#@title 2. Download pharokka phold databases\n",
        "\n",
        "#@markdown This cell downloads the pharokka then the phold database. It will take some time (5-10 minutes probably). Please be patient.\n",
        "\n",
        "\n",
        "%%time\n",
        "import os\n",
        "print(\"Downloading pharokka database. This will take a few minutes. Please be patient :)\")\n",
        "os.system(\"install_databases.py -o pharokka_db\")\n",
        "print(\"Downloading phold database. This will take a few minutes. Please be patient :)\")\n",
        "os.system(\"phold install -d phold_db\")\n",
        "\n",
        "\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 3,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "Sjdpu6R-Kig9",
        "outputId": "4a07ee8d-2290-459e-d899-dcd337aeec26"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Input file NC_043029.fasta exists\n",
            "Running pharokka\n",
            "pharokka completed successfully.\n",
            "Your output is in output_pharokka.\n",
            "Zipping the output directory so you can download it all in one go.\n",
            "Output directory has been zipped to output_pharokka.zip\n",
            "CPU times: user 147 ms, sys: 19.6 ms, total: 167 ms\n",
            "Wall time: 32.8 s\n"
          ]
        }
      ],
      "source": [
        "#@title 3. Run Pharokka\n",
        "\n",
        "#@markdown First, upload your phage(s) as a nucleotide input FASTA file\n",
        "\n",
        "#@markdown Click on the folder icon to the left and use the file upload button.\n",
        "\n",
        "#@markdown Once it is uploaded, write the file name in the INPUT_FILE field on the right.\n",
        "\n",
        "#@markdown Then provide a directory for pharokka's output using PHAROKKA_OUT_DIR.\n",
        "#@markdown The default is 'output_pharokka'.\n",
        "\n",
        "#@markdown Then type in a gene prediction tool for pharokka.\n",
        "#@markdown Please choose either 'phanotate', 'prodigal', or 'prodigal-gv'.\n",
        "\n",
        "#@markdown You can also provide a prefix for your output files with PHAROKKA_PREFIX.\n",
        "#@markdown If you provide nothing it will default to 'pharokka'.\n",
        "\n",
        "#@markdown You can also provide a locus tag for your output files.\n",
        "#@markdown If you provide nothing it will generate a random locus tag.\n",
        "\n",
        "#@markdown You can click FAST to turn off --fast.\n",
        "#@markdown By default it is True so that Pharokka runs faster in the Colab environment.\n",
        "\n",
        "#@markdown You can click META to turn on --meta if you have multiple phages in your input.\n",
        "\n",
        "#@markdown You can click META_HMM to turn on --meta_hmm.\n",
        "\n",
        "#@markdown You can click FORCE to overwrite the output directory.\n",
        "#@markdown This may be useful if your earlier pharokka run has crashed for whatever reason.\n",
        "\n",
        "#@markdown The results of Pharokka will be in the folder icon on the left hand panel.\n",
        "#@markdown Additionally, it will be zipped so you can download the whole directory.\n",
        "\n",
        "#@markdown The file to download is PHAROKKA_OUT_DIR.zip, where PHAROKKA_OUT_DIR is what you provided\n",
        "\n",
        "#@markdown If you do not see the output directory,\n",
        "#@markdown refresh the window by either clicking the folder with the refresh icon below \"Files\"\n",
        "#@markdown or double click and select \"Refresh\".\n",
        "\n",
        "\n",
        "%%time\n",
        "import os\n",
        "import sys\n",
        "import subprocess\n",
        "import zipfile\n",
        "INPUT_FILE = '' #@param {type:\"string\"}\n",
        "\n",
        "if os.path.exists(INPUT_FILE):\n",
        "    print(f\"Input file {INPUT_FILE} exists\")\n",
        "else:\n",
        "    print(f\"Error: File {INPUT_FILE} does not exist\")\n",
        "    print(f\"Please check the spelling and that you have uploaded it correctly\")\n",
        "    sys.exit(1)\n",
        "\n",
        "PHAROKKA_OUT_DIR = 'output_pharokka'  #@param {type:\"string\"}\n",
        "GENE_PREDICTOR = 'phanotate'  #@param {type:\"string\"}\n",
        "allowed_gene_predictors = ['phanotate', 'prodigal', 'prodigal-gv']\n",
        "# Check if the input parameter is valid\n",
        "if GENE_PREDICTOR.lower() not in allowed_gene_predictors:\n",
        "    raise ValueError(\"Invalid GENE_PREDICTOR. Please choose from: 'phanotate', 'prodigal', 'prodigal-gv'.\")\n",
        "\n",
        "PHAROKKA_PREFIX = 'pharokka'  #@param {type:\"string\"}\n",
        "LOCUS_TAG = 'Default'  #@param {type:\"string\"}\n",
        "FAST = True  #@param {type:\"boolean\"}\n",
        "META = False  #@param {type:\"boolean\"}\n",
        "META_HMM = False  #@param {type:\"boolean\"}\n",
        "FORCE = True  #@param {type:\"boolean\"}\n",
        "\n",
        "\n",
        "# Construct the command\n",
        "command = f\"pharokka.py -d pharokka_db -i {INPUT_FILE} -t 4 -o {PHAROKKA_OUT_DIR} -p {PHAROKKA_PREFIX} -l {LOCUS_TAG} -g {GENE_PREDICTOR}\"\n",
        "\n",
        "if FORCE is True:\n",
        "  command = f\"{command} -f\"\n",
        "\n",
        "if FAST is True:\n",
        "  command = f\"{command} --fast\"\n",
        "\n",
        "if META is True:\n",
        "  command = f\"{command} -m\"\n",
        "\n",
        "if META_HMM is True:\n",
        "  command = f\"{command} --meta_hmm\"\n",
        "\n",
        "# Execute the command\n",
        "try:\n",
        "    print(\"Running pharokka\")\n",
        "    subprocess.run(command, shell=True, check=True)\n",
        "    print(\"pharokka completed successfully.\")\n",
        "    print(f\"Your output is in {PHAROKKA_OUT_DIR}.\")\n",
        "    print(f\"Zipping the output directory so you can download it all in one go.\")\n",
        "\n",
        "    zip_filename = f\"{PHAROKKA_OUT_DIR}.zip\"\n",
        "\n",
        "    # Zip the contents of the output directory\n",
        "    with zipfile.ZipFile(zip_filename, 'w', zipfile.ZIP_DEFLATED) as zipf:\n",
        "        for root, dirs, files in os.walk(PHAROKKA_OUT_DIR):\n",
        "            for file in files:\n",
        "                zipf.write(os.path.join(root, file), os.path.relpath(os.path.join(root, file), PHAROKKA_OUT_DIR))\n",
        "    print(f\"Output directory has been zipped to {zip_filename}\")\n",
        "\n",
        "\n",
        "except subprocess.CalledProcessError as e:\n",
        "    print(f\"Error occurred: {e}\")\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 4,
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "9QfjP3q-Q04f",
        "outputId": "91bf9e52-d5dc-4d80-8c61-a5db46b75535"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Running phold\n",
            "phold completed successfully.\n",
            "Your output is in output_phold.\n",
            "Zipping the output directory so you can download it all in one go.\n",
            "Output directory has been zipped to output_phold.zip\n",
            "CPU times: user 451 ms, sys: 61.9 ms, total: 513 ms\n",
            "Wall time: 1min 48s\n"
          ]
        }
      ],
      "source": [
        "#@title 4. Run phold\n",
        "\n",
        "#@markdown This cell will run phold on the output of cell 3's Pharokka run\n",
        "\n",
        "#@markdown You do not need to provide any further input files\n",
        "\n",
        "#@markdown You can now provide a directory for phold's output with PHOLD_OUT_DIR.\n",
        "#@markdown The default is 'output_phold'.\n",
        "\n",
        "#@markdown You can also provide a prefix for your output files with PHOLD_PREFIX.\n",
        "#@markdown If you provide nothing it will default to 'phold'.\n",
        "\n",
        "#@markdown You can click FORCE to overwrite the output directory with .\n",
        "#@markdown This may be useful if your earlier phold run has crashed for whatever reason.\n",
        "\n",
        "#@markdown If your input has multiple phages, you can click SEPARATE.\n",
        "#@markdown This will output separate GenBank files in the output directory.\n",
        "\n",
        "#@markdown The results of Phold will be in the folder icon on the left hand panel.\n",
        "#@markdown Additionally, it will be zipped so you can download the whole directory.\n",
        "\n",
        "#@markdown The file to download is PHOLD_OUT_DIR.zip, where PHOLD_OUT_DIR is what you provided\n",
        "\n",
        "#@markdown If you do not see the output directory,\n",
        "#@markdown refresh the window by either clicking the folder with the refresh icon below \"Files\"\n",
        "#@markdown or double click and select \"Refresh\".\n",
        "\n",
        "\n",
        "%%time\n",
        "import os\n",
        "import subprocess\n",
        "import zipfile\n",
        "\n",
        "# phold input is pharokka output\n",
        "PHOLD_INPUT = f\"{PHAROKKA_OUT_DIR}/{PHAROKKA_PREFIX}.gbk\"\n",
        "PHOLD_OUT_DIR = 'output_phold'  #@param {type:\"string\"}\n",
        "PHOLD_PREFIX = 'phold'  #@param {type:\"string\"}\n",
        "FORCE = True  #@param {type:\"boolean\"}\n",
        "SEPARATE = False  #@param {type:\"boolean\"}\n",
        "\n",
        "# Construct the command\n",
        "command = f\"phold run -i {PHOLD_INPUT} -t 4 -o {PHOLD_OUT_DIR} -p {PHOLD_PREFIX} -d phold_db\"\n",
        "\n",
        "if FORCE is True:\n",
        "  command = f\"{command} -f\"\n",
        "if SEPARATE is True:\n",
        "  command = f\"{command} --separate\"\n",
        "\n",
        "\n",
        "# Execute the command\n",
        "try:\n",
        "    print(\"Running phold\")\n",
        "    subprocess.run(command, shell=True, check=True)\n",
        "    print(\"phold completed successfully.\")\n",
        "    print(f\"Your output is in {PHOLD_OUT_DIR}.\")\n",
        "    print(f\"Zipping the output directory so you can download it all in one go.\")\n",
        "\n",
        "    zip_filename = f\"{PHOLD_OUT_DIR}.zip\"\n",
        "\n",
        "    # Zip the contents of the output directory\n",
        "    with zipfile.ZipFile(zip_filename, 'w', zipfile.ZIP_DEFLATED) as zipf:\n",
        "        for root, dirs, files in os.walk(PHOLD_OUT_DIR):\n",
        "            for file in files:\n",
        "                zipf.write(os.path.join(root, file), os.path.relpath(os.path.join(root, file), PHOLD_OUT_DIR))\n",
        "    print(f\"Output directory has been zipped to {zip_filename}\")\n",
        "\n",
        "\n",
        "except subprocess.CalledProcessError as e:\n",
        "    print(f\"Error occurred: {e}\")\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "\n"
      ]
    },
    {
      "cell_type": "code",
      "source": [
        "#@title 5. Install phynteny\n",
        "\n",
        "#@markdown This cell installs phynteny and downloads the models. It will take a few minutes. Please be patient\n",
        "%%bash\n",
        "PHYNTENY_VERSION=\"0.1.13\"\n",
        "NUMPY_VERSION=\"1.26.4\"\n",
        "\n",
        "if [ ! -f PHYNTENY_READY ]; then\n",
        "  echo \"installing phynteny\"\n",
        "  pip install phynteny==${PHYNTENY_VERSION} numpy==${NUMPY_VERSION}\n",
        "  echo \"Downloading phynteny models\"\n",
        "  install_models -o phynteny_models\n",
        "  touch PHYNTENY_READY\n",
        "fi\n"
      ],
      "metadata": {
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "id": "1eUYA415PNRX",
        "outputId": "80fb0086-058e-42f0-a1c2-9f18cc3823b5"
      },
      "execution_count": 5,
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "installing phynteny\n",
            "Collecting phynteny==0.1.13\n",
            "  Downloading phynteny-0.1.13-py3-none-any.whl.metadata (7.9 kB)\n",
            "Collecting numpy==1.26.4\n",
            "  Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)\n",
            "Requirement already satisfied: biopython>=1.79 in /usr/local/lib/python3.10/site-packages (from phynteny==0.1.13) (1.81)\n",
            "Collecting scikit-learn<=1.2.2 (from phynteny==0.1.13)\n",
            "  Downloading scikit_learn-1.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)\n",
            "Requirement already satisfied: pandas in /usr/local/lib/python3.10/site-packages (from phynteny==0.1.13) (2.2.3)\n",
            "Requirement already satisfied: click in /usr/local/lib/python3.10/site-packages (from phynteny==0.1.13) (8.1.7)\n",
            "Collecting joblib (from phynteny==0.1.13)\n",
            "  Downloading joblib-1.4.2-py3-none-any.whl.metadata (5.4 kB)\n",
            "Requirement already satisfied: loguru in /usr/local/lib/python3.10/site-packages (from phynteny==0.1.13) (0.7.2)\n",
            "Collecting tensorflow==2.9.1 (from phynteny==0.1.13)\n",
            "  Downloading tensorflow-2.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)\n",
            "Requirement already satisfied: alive-progress>=3.0.1 in /usr/local/lib/python3.10/site-packages (from phynteny==0.1.13) (3.1.5)\n",
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            "Collecting absl-py>=1.0.0 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
            "  Downloading absl_py-2.1.0-py3-none-any.whl.metadata (2.3 kB)\n",
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            "Collecting flatbuffers<2,>=1.12 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
            "  Downloading flatbuffers-1.12-py2.py3-none-any.whl.metadata (872 bytes)\n",
            "Collecting gast<=0.4.0,>=0.2.1 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
            "  Downloading gast-0.4.0-py3-none-any.whl.metadata (1.1 kB)\n",
            "Collecting google-pasta>=0.1.1 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
            "  Downloading google_pasta-0.2.0-py3-none-any.whl.metadata (814 bytes)\n",
            "Collecting grpcio<2.0,>=1.24.3 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
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            "Collecting keras<2.10.0,>=2.9.0rc0 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
            "  Downloading keras-2.9.0-py2.py3-none-any.whl.metadata (1.3 kB)\n",
            "Collecting keras-preprocessing>=1.1.1 (from tensorflow==2.9.1->phynteny==0.1.13)\n",
            "  Downloading Keras_Preprocessing-1.1.2-py2.py3-none-any.whl.metadata (1.9 kB)\n",
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            "Installing collected packages: tensorboard-plugin-wit, libclang, keras, flatbuffers, wrapt, werkzeug, threadpoolctl, termcolor, tensorflow-io-gcs-filesystem, tensorflow-estimator, tensorboard-data-server, pyasn1, protobuf, opt-einsum, oauthlib, numpy, markdown, joblib, grpcio, google-pasta, gast, cachetools, astunparse, absl-py, rsa, requests-oauthlib, pyasn1-modules, keras-preprocessing, scikit-learn, google-auth, google-auth-oauthlib, tensorboard, tensorflow, phynteny\n",
            "  Attempting uninstall: numpy\n",
            "    Found existing installation: numpy 2.1.3\n",
            "    Uninstalling numpy-2.1.3:\n",
            "      Successfully uninstalled numpy-2.1.3\n",
            "Successfully installed absl-py-2.1.0 astunparse-1.6.3 cachetools-5.5.0 flatbuffers-1.12 gast-0.4.0 google-auth-2.36.0 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.68.0 joblib-1.4.2 keras-2.9.0 keras-preprocessing-1.1.2 libclang-18.1.1 markdown-3.7 numpy-1.26.4 oauthlib-3.2.2 opt-einsum-3.4.0 phynteny-0.1.13 protobuf-3.19.6 pyasn1-0.6.1 pyasn1-modules-0.4.1 requests-oauthlib-2.0.0 rsa-4.9 scikit-learn-1.2.2 tensorboard-2.9.1 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tensorflow-2.9.1 tensorflow-estimator-2.9.0 tensorflow-io-gcs-filesystem-0.37.1 termcolor-2.5.0 threadpoolctl-3.5.0 werkzeug-3.1.3 wrapt-1.17.0\n",
            "Downloading phynteny models\n",
            "Downloading Phynteny models to phynteny_models\n",
            "Phynteny models are missing.\n",
            "Some models are missing.\n",
            "Downloading Phynteny Models from https://zenodo.org/record/8198288/files/phynteny_models_v0.1.11.tar.gz.\n",
            "path\n",
            "https://zenodo.org/record/8198288/files/phynteny_models_v0.1.11.tar.gz\n",
            "|████████████████████████████████████████| 381.6M/381.6M [100%] in 7:20.9 (865.49k/s) \n",
            "Phynteny Models tarball download OK: 364c1eab8cda872a8757c1187a5c2b53\n",
            "Extracting Phynteny Models tarball: file=phynteny_models/phynteny_models_v0.1.11.tar.gz, output=phynteny_models\n",
            "Done.\n"
          ]
        }
      ]
    },
    {
      "cell_type": "code",
      "execution_count": 6,
      "metadata": {
        "id": "BlPLP3vlhWYs",
        "colab": {
          "base_uri": "https://localhost:8080/"
        },
        "outputId": "e4cc231e-fbc5-4b2d-fb7c-38e102efc849"
      },
      "outputs": [
        {
          "output_type": "stream",
          "name": "stdout",
          "text": [
            "Running phynteny\n",
            "phynteny completed successfully.\n",
            "Your output is in output_phynteny.\n",
            "Zipping the output directory so you can download it all in one go.\n",
            "Output directory has been zipped to output_phynteny.zip\n",
            "CPU times: user 182 ms, sys: 37.7 ms, total: 220 ms\n",
            "Wall time: 45.6 s\n"
          ]
        }
      ],
      "source": [
        "#@title 6. Run Phynteny\n",
        "\n",
        "#@markdown This cell will run phynteny on the output of cell 4's Phold run to predict the function of remaining hypothetical proteins\n",
        "\n",
        "#@markdown You do not need to provide any further input files\n",
        "\n",
        "#@markdown You can now provide a directory for phynteny's output with PHYNTENY_OUT_DIR.\n",
        "#@markdown The default is 'output_phynteny'.\n",
        "\n",
        "#@markdown You can click FORCE to overwrite the output directory with .\n",
        "#@markdown This may be useful if your phynteny run has crashed for whatever reason.\n",
        "\n",
        "#@markdown The results of Phynteny will be in the folder icon on the left hand panel.\n",
        "#@markdown Additionally, it will be zipped so you can download the whole directory.\n",
        "\n",
        "#@markdown The file to download is PHYNTENY_OUT_DIR.zip, where PHYNTENY_OUT_DIR is what you provided\n",
        "\n",
        "#@markdown If you do not see the output directory,\n",
        "#@markdown refresh the window by either clicking the folder with the refresh icon below \"Files\"\n",
        "#@markdown or double click and select \"Refresh\".\n",
        "\n",
        "\n",
        "%%time\n",
        "import os\n",
        "import subprocess\n",
        "import zipfile\n",
        "\n",
        "# phynteny input is pharokka output\n",
        "PHYNTENY_INPUT = f\"{PHOLD_OUT_DIR}/{PHOLD_PREFIX}.gbk\"\n",
        "PHYNTENY_OUT_DIR = 'output_phynteny'  #@param {type:\"string\"}\n",
        "FORCE = False  #@param {type:\"boolean\"}\n",
        "\n",
        "# Construct the command\n",
        "command = f\"phynteny {PHYNTENY_INPUT} -m phynteny_models -o {PHYNTENY_OUT_DIR}\"\n",
        "\n",
        "if FORCE is True:\n",
        "  command = f\"{command} -f\"\n",
        "\n",
        "\n",
        "# Execute the command\n",
        "try:\n",
        "    print(\"Running phynteny\")\n",
        "    subprocess.run(command, shell=True, check=True)\n",
        "    print(\"phynteny completed successfully.\")\n",
        "    print(f\"Your output is in {PHYNTENY_OUT_DIR}.\")\n",
        "    print(f\"Zipping the output directory so you can download it all in one go.\")\n",
        "\n",
        "    zip_filename = f\"{PHYNTENY_OUT_DIR}.zip\"\n",
        "\n",
        "    # Zip the contents of the output directory\n",
        "    with zipfile.ZipFile(zip_filename, 'w', zipfile.ZIP_DEFLATED) as zipf:\n",
        "        for root, dirs, files in os.walk(PHYNTENY_OUT_DIR):\n",
        "            for file in files:\n",
        "                zipf.write(os.path.join(root, file), os.path.relpath(os.path.join(root, file), PHYNTENY_OUT_DIR))\n",
        "    print(f\"Output directory has been zipped to {zip_filename}\")\n",
        "\n",
        "\n",
        "except subprocess.CalledProcessError as e:\n",
        "    print(f\"Error occurred: {e}\")\n",
        "\n",
        "\n",
        "\n",
        "\n",
        "\n"
      ]
    }
  ],
  "metadata": {
    "colab": {
      "provenance": [],
      "gpuType": "T4",
      "authorship_tag": "ABX9TyOn+XbE6ByCGMHehzgMhZLM",
      "include_colab_link": true
    },
    "kernelspec": {
      "display_name": "Python 3",
      "name": "python3"
    },
    "language_info": {
      "name": "python"
    },
    "accelerator": "GPU"
  },
  "nbformat": 4,
  "nbformat_minor": 0
}