.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_zenodo.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_auto_examples_plot_zenodo.py>`
        to download the full example code or to run this example in your browser via JupyterLite.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_plot_zenodo.py:


Loading a RDS file from a URL
=============================

A simple example showing how to read a dataset in the RDS format from a URL.

.. GENERATED FROM PYTHON SOURCE LINES 8-11

.. code-block:: Python


    # sphinx_gallery_thumbnail_path = '_static/download.png'








.. GENERATED FROM PYTHON SOURCE LINES 12-15

If the data to read is accesible at a particular URL, we can open it as a
file using the function :external+python:func:`urllib.request.urlopen`.
Thus, we need to import that function as well as the rdata package.

.. GENERATED FROM PYTHON SOURCE LINES 15-20

.. code-block:: Python


    from urllib.request import urlopen

    import rdata








.. GENERATED FROM PYTHON SOURCE LINES 21-25

For this example we will use a dataset hosted at
`Zenodo <https://zenodo.org/records/7425539>`_.
This is a small dataset containing information about some fungal pathogens.


.. GENERATED FROM PYTHON SOURCE LINES 25-29

.. code-block:: Python

    dataset_url = (
        "https://zenodo.org/records/7425539/files/core_fungal_pathogens.rds"
    )








.. GENERATED FROM PYTHON SOURCE LINES 30-33

The object resulting from calling
:external+python:func:`~urllib.request.urlopen` can be then
passed to :func:`~rdata.parser.parse_file` as if it were a normal file.

.. GENERATED FROM PYTHON SOURCE LINES 33-37

.. code-block:: Python


    with urlopen(dataset_url) as dataset:
        parsed = rdata.parser.parse_file(dataset)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/rdata/envs/latest/lib/python3.11/site-packages/rdata/parser/_parser.py:1257: UserWarning: Unknown file type: assumed RDS
      warnings.warn("Unknown file type: assumed RDS")  # noqa: B028




.. GENERATED FROM PYTHON SOURCE LINES 38-43

RDS files do not have a special magic number that identifies them.
Thus, when reading a RDS file, rdata has to suppose that the file is a valid
RDS file, and warns about that.
We can omit this warning by passing manually the extension of the file
instead.

.. GENERATED FROM PYTHON SOURCE LINES 43-46

.. code-block:: Python

    with urlopen(dataset_url) as dataset:
        parsed = rdata.parser.parse_file(dataset, extension=".rds")








.. GENERATED FROM PYTHON SOURCE LINES 47-54

This parsed object contains a lossless representation of the internal data
contained in the file.
This data mimics the internal format used in R, and is thus not directly
usable.
However, we can retrieve some information about the file that will be lost
after the conversion to a Python object, such as the version of the format
employed or the encoding used for the strings.

.. GENERATED FROM PYTHON SOURCE LINES 54-58

.. code-block:: Python


    print(parsed.versions.format)
    print(parsed.extra.encoding)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    3
    UTF-8




.. GENERATED FROM PYTHON SOURCE LINES 59-61

In order to convert it to Python objects we need to use the function
:func:`rdata.conversion.convert`.

.. GENERATED FROM PYTHON SOURCE LINES 61-63

.. code-block:: Python

    converted = rdata.conversion.convert(parsed)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/rdata/envs/latest/lib/python3.11/site-packages/rdata/conversion/_conversion.py:900: UserWarning: Missing constructor for R class "Date". The underlying R object is returned instead.
      warnings.warn(




.. GENERATED FROM PYTHON SOURCE LINES 64-67

RDS files contain just one R object.
In this particular case, it is a R dataframe object, that will be converted
to a Pandas dataframe by default.

.. GENERATED FROM PYTHON SOURCE LINES 67-69

.. code-block:: Python

    converted






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }

        .dataframe tbody tr th {
            vertical-align: top;
        }

        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>species_taxid</th>
          <th>assembly_accession</th>
          <th>refseq_category</th>
          <th>taxid</th>
          <th>organism_name</th>
          <th>infraspecific_name</th>
          <th>assembly_level</th>
          <th>seq_rel_date</th>
          <th>asm_name</th>
          <th>ftp_path</th>
          <th>Species</th>
          <th>source.taxid</th>
          <th>source.name</th>
          <th>human.pathogen</th>
          <th>animal.pathogen</th>
          <th>plant.pathogen</th>
          <th>plant.host</th>
          <th>putative.human.host</th>
          <th>putative.animal.host</th>
          <th>putative.plant.host</th>
          <th>human.pathogen.source</th>
          <th>animal.pathogen.source</th>
          <th>plant.pathogen.source</th>
          <th>plant.host.source</th>
          <th>putative.human.host.source</th>
          <th>putative.animal.host.source</th>
          <th>putative.plant.host.source</th>
          <th>atlas.synonym.name</th>
          <th>atlas.synonym.taxid</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>1</th>
          <td>4754</td>
          <td>GCA_001477545.1</td>
          <td>representative genome</td>
          <td>1408658</td>
          <td>Pneumocystis carinii B80</td>
          <td>strain=B80</td>
          <td>Contig</td>
          <td>16791.0</td>
          <td>Pneu_cari_B80_V3</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Pneumocystis carinii</td>
          <td></td>
          <td>Pneumocystis carinii</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td></td>
          <td>Cissé, O. H., Ma, L., Dekker, J. P., Khil, P. ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>3</th>
          <td>4837</td>
          <td>GCA_001638985.2</td>
          <td>representative genome</td>
          <td>763407</td>
          <td>Phycomyces blakesleeanus NRRL 1555(-)</td>
          <td>strain=NRRL 1555(-)</td>
          <td>Scaffold</td>
          <td>16927.0</td>
          <td>Phybl2</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Phycomyces blakesleeanus</td>
          <td>4837</td>
          <td>Phycomyces blakesleeanus</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td></td>
          <td></td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>4</th>
          <td>4839</td>
          <td>GCA_000611695.1</td>
          <td>representative genome</td>
          <td>1031333</td>
          <td>Rhizomucor miehei CAU432</td>
          <td>strain=CAU432</td>
          <td>Scaffold</td>
          <td>16160.0</td>
          <td>RhzM_1.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Rhizomucor miehei</td>
          <td>4839</td>
          <td>Rhizomucor miehei</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>Taylor, L. H., Latham, S. M., &amp; Woolhouse, M. ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>5</th>
          <td>4840</td>
          <td>GCA_900175165.2</td>
          <td>representative genome</td>
          <td>4840</td>
          <td>Rhizomucor pusillus</td>
          <td></td>
          <td>Scaffold</td>
          <td>17781.0</td>
          <td>FCH_5_7</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/9...</td>
          <td>Rhizomucor pusillus</td>
          <td>4840</td>
          <td>Rhizomucor pusillus</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>Taylor, L. H., Latham, S. M., &amp; Woolhouse, M. ...</td>
          <td>Smith, J.M. (2006). Fungal Pathogens of Nonhum...</td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>6</th>
          <td>4841</td>
          <td>GCA_000697255.1</td>
          <td>representative genome</td>
          <td>1357677</td>
          <td>Mucor racemosus B9645</td>
          <td>strain=B9645</td>
          <td>Contig</td>
          <td>16223.0</td>
          <td>MucRacB9645-1.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Mucor racemosus</td>
          <td>4841</td>
          <td>Mucor racemosus</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>True</td>
          <td>Taylor, L. H., Latham, S. M., &amp; Woolhouse, M. ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>...</th>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
        </tr>
        <tr>
          <th>1885</th>
          <td>2714763</td>
          <td>GCA_001636795.1</td>
          <td>representative genome</td>
          <td>1081108</td>
          <td>Akanthomyces lecanii RCEF 1005</td>
          <td>strain=RCEF 1005</td>
          <td>Scaffold</td>
          <td>16925.0</td>
          <td>LEL 1.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Akanthomyces lecanii</td>
          <td></td>
          <td>Verticillium lecanii</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td></td>
          <td>D. Chandler, G. Davidson, J. K. Pell, B. V. Ba...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1886</th>
          <td>2747968</td>
          <td>GCA_000151355.1</td>
          <td>representative genome</td>
          <td>660122</td>
          <td>Fusarium vanettenii 77-13-4</td>
          <td></td>
          <td>Scaffold</td>
          <td>14483.0</td>
          <td>v2.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Fusarium vanettenii</td>
          <td>70791</td>
          <td>Fusarium solani</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1888</th>
          <td>2778779</td>
          <td>GCA_004016085.1</td>
          <td>representative genome</td>
          <td>2778779</td>
          <td>Claviceps quebecensis</td>
          <td></td>
          <td>Contig</td>
          <td>17910.0</td>
          <td>ASM401608v1</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Claviceps quebecensis</td>
          <td>2778779</td>
          <td>Claviceps quebecensis</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td></td>
          <td></td>
          <td>Farr, D.F., &amp; Rossman, A.Y. Fungal Databases, ...</td>
          <td>Farr, D.F., &amp; Rossman, A.Y. Fungal Databases, ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1890</th>
          <td>2822231</td>
          <td>GCA_001910725.1</td>
          <td>representative genome</td>
          <td>2822231</td>
          <td>Phanerodontia chrysosporium</td>
          <td>strain=ATCC 20696</td>
          <td>Contig</td>
          <td>17155.0</td>
          <td>ASM191072v1</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Phanerodontia chrysosporium</td>
          <td>2822231</td>
          <td>Phanerodontia chrysosporium</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>Anuradha Chowdhary, Shallu Kathuria, Kshitij A...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1891</th>
          <td>2867405</td>
          <td>GCA_900239735.1</td>
          <td>representative genome</td>
          <td>546991</td>
          <td>Blumeria hordei DH14</td>
          <td>cultivar=Golden Promise</td>
          <td>Scaffold</td>
          <td>17621.0</td>
          <td>BGH_DH14_v4</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/9...</td>
          <td>Blumeria hordei</td>
          <td>62688</td>
          <td>Erysiphe graminis</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td></td>
          <td></td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
      </tbody>
    </table>
    <p>954 rows × 29 columns</p>
    </div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 70-73

As usually we just want to parse and convert a given dataset, the convenience
functions :func:`rdata.read_rds` and :func:`rdata.read_rda` can be used with
that purpose.

.. GENERATED FROM PYTHON SOURCE LINES 73-77

.. code-block:: Python

    with urlopen(dataset_url) as dataset:
        data = rdata.read_rds(dataset)

    data




.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /home/docs/checkouts/readthedocs.org/user_builds/rdata/envs/latest/lib/python3.11/site-packages/rdata/conversion/_conversion.py:900: UserWarning: Missing constructor for R class "Date". The underlying R object is returned instead.
      warnings.warn(


.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }

        .dataframe tbody tr th {
            vertical-align: top;
        }

        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>species_taxid</th>
          <th>assembly_accession</th>
          <th>refseq_category</th>
          <th>taxid</th>
          <th>organism_name</th>
          <th>infraspecific_name</th>
          <th>assembly_level</th>
          <th>seq_rel_date</th>
          <th>asm_name</th>
          <th>ftp_path</th>
          <th>Species</th>
          <th>source.taxid</th>
          <th>source.name</th>
          <th>human.pathogen</th>
          <th>animal.pathogen</th>
          <th>plant.pathogen</th>
          <th>plant.host</th>
          <th>putative.human.host</th>
          <th>putative.animal.host</th>
          <th>putative.plant.host</th>
          <th>human.pathogen.source</th>
          <th>animal.pathogen.source</th>
          <th>plant.pathogen.source</th>
          <th>plant.host.source</th>
          <th>putative.human.host.source</th>
          <th>putative.animal.host.source</th>
          <th>putative.plant.host.source</th>
          <th>atlas.synonym.name</th>
          <th>atlas.synonym.taxid</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>1</th>
          <td>4754</td>
          <td>GCA_001477545.1</td>
          <td>representative genome</td>
          <td>1408658</td>
          <td>Pneumocystis carinii B80</td>
          <td>strain=B80</td>
          <td>Contig</td>
          <td>16791.0</td>
          <td>Pneu_cari_B80_V3</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Pneumocystis carinii</td>
          <td></td>
          <td>Pneumocystis carinii</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td></td>
          <td>Cissé, O. H., Ma, L., Dekker, J. P., Khil, P. ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>3</th>
          <td>4837</td>
          <td>GCA_001638985.2</td>
          <td>representative genome</td>
          <td>763407</td>
          <td>Phycomyces blakesleeanus NRRL 1555(-)</td>
          <td>strain=NRRL 1555(-)</td>
          <td>Scaffold</td>
          <td>16927.0</td>
          <td>Phybl2</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Phycomyces blakesleeanus</td>
          <td>4837</td>
          <td>Phycomyces blakesleeanus</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td></td>
          <td></td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>4</th>
          <td>4839</td>
          <td>GCA_000611695.1</td>
          <td>representative genome</td>
          <td>1031333</td>
          <td>Rhizomucor miehei CAU432</td>
          <td>strain=CAU432</td>
          <td>Scaffold</td>
          <td>16160.0</td>
          <td>RhzM_1.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Rhizomucor miehei</td>
          <td>4839</td>
          <td>Rhizomucor miehei</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>Taylor, L. H., Latham, S. M., &amp; Woolhouse, M. ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>5</th>
          <td>4840</td>
          <td>GCA_900175165.2</td>
          <td>representative genome</td>
          <td>4840</td>
          <td>Rhizomucor pusillus</td>
          <td></td>
          <td>Scaffold</td>
          <td>17781.0</td>
          <td>FCH_5_7</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/9...</td>
          <td>Rhizomucor pusillus</td>
          <td>4840</td>
          <td>Rhizomucor pusillus</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>Taylor, L. H., Latham, S. M., &amp; Woolhouse, M. ...</td>
          <td>Smith, J.M. (2006). Fungal Pathogens of Nonhum...</td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>6</th>
          <td>4841</td>
          <td>GCA_000697255.1</td>
          <td>representative genome</td>
          <td>1357677</td>
          <td>Mucor racemosus B9645</td>
          <td>strain=B9645</td>
          <td>Contig</td>
          <td>16223.0</td>
          <td>MucRacB9645-1.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Mucor racemosus</td>
          <td>4841</td>
          <td>Mucor racemosus</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>True</td>
          <td>Taylor, L. H., Latham, S. M., &amp; Woolhouse, M. ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>...</th>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
        </tr>
        <tr>
          <th>1885</th>
          <td>2714763</td>
          <td>GCA_001636795.1</td>
          <td>representative genome</td>
          <td>1081108</td>
          <td>Akanthomyces lecanii RCEF 1005</td>
          <td>strain=RCEF 1005</td>
          <td>Scaffold</td>
          <td>16925.0</td>
          <td>LEL 1.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Akanthomyces lecanii</td>
          <td></td>
          <td>Verticillium lecanii</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td></td>
          <td>D. Chandler, G. Davidson, J. K. Pell, B. V. Ba...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1886</th>
          <td>2747968</td>
          <td>GCA_000151355.1</td>
          <td>representative genome</td>
          <td>660122</td>
          <td>Fusarium vanettenii 77-13-4</td>
          <td></td>
          <td>Scaffold</td>
          <td>14483.0</td>
          <td>v2.0</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Fusarium vanettenii</td>
          <td>70791</td>
          <td>Fusarium solani</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1888</th>
          <td>2778779</td>
          <td>GCA_004016085.1</td>
          <td>representative genome</td>
          <td>2778779</td>
          <td>Claviceps quebecensis</td>
          <td></td>
          <td>Contig</td>
          <td>17910.0</td>
          <td>ASM401608v1</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Claviceps quebecensis</td>
          <td>2778779</td>
          <td>Claviceps quebecensis</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td></td>
          <td></td>
          <td>Farr, D.F., &amp; Rossman, A.Y. Fungal Databases, ...</td>
          <td>Farr, D.F., &amp; Rossman, A.Y. Fungal Databases, ...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1890</th>
          <td>2822231</td>
          <td>GCA_001910725.1</td>
          <td>representative genome</td>
          <td>2822231</td>
          <td>Phanerodontia chrysosporium</td>
          <td>strain=ATCC 20696</td>
          <td>Contig</td>
          <td>17155.0</td>
          <td>ASM191072v1</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/0...</td>
          <td>Phanerodontia chrysosporium</td>
          <td>2822231</td>
          <td>Phanerodontia chrysosporium</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>Anuradha Chowdhary, Shallu Kathuria, Kshitij A...</td>
          <td></td>
          <td></td>
          <td></td>
          <td>Conrad L Schoch, Stacy Ciufo, Mikhail Domrache...</td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
        <tr>
          <th>1891</th>
          <td>2867405</td>
          <td>GCA_900239735.1</td>
          <td>representative genome</td>
          <td>546991</td>
          <td>Blumeria hordei DH14</td>
          <td>cultivar=Golden Promise</td>
          <td>Scaffold</td>
          <td>17621.0</td>
          <td>BGH_DH14_v4</td>
          <td>https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/9...</td>
          <td>Blumeria hordei</td>
          <td>62688</td>
          <td>Erysiphe graminis</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td>True</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
          <td>True</td>
          <td></td>
          <td></td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td>Tao Lu, Bo Yao, Chi Zhang, DFVF: database of f...</td>
          <td></td>
          <td></td>
          <td>Wardeh, M., Risley, C., McIntyre, M. et al. Da...</td>
          <td>&lt;NA&gt;</td>
          <td>&lt;NA&gt;</td>
        </tr>
      </tbody>
    </table>
    <p>954 rows × 29 columns</p>
    </div>
    </div>
    <br />
    <br />


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 5.642 seconds)


.. _sphx_glr_download_auto_examples_plot_zenodo.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: lite-badge

      .. image:: images/jupyterlite_badge_logo.svg
        :target: ../lite/lab/index.html?path=auto_examples/plot_zenodo.ipynb
        :alt: Launch JupyterLite
        :width: 150 px

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_zenodo.ipynb <plot_zenodo.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_zenodo.py <plot_zenodo.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_zenodo.zip <plot_zenodo.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_