Add As1

malariagen_data/__init__.py

@@ -2,6 +2,7 @@
 from .af1 import Af1
 from .ag3 import Ag3
 from .amin1 import Amin1
+from .as1 import As1
 from .anopheles import AnophelesDataResource, Region
 from .pf7 import Pf7
 from .pf8 import Pf8

malariagen_data/anoph/base.py

@@ -437,12 +437,25 @@ def sample_sets(
             # Ensure no duplicates.
             releases = sorted(set(release))
 
-            # Retrieve and concatenate sample sets from multiple releases.
-            df = pd.concat(
-                [self.sample_sets(release=r) for r in releases],
-                axis=0,
-                ignore_index=True,
-            )
+            # Add each release's sample sets DataFrame to a list.
+            sample_set_dfs = []
+            for release in releases:
+                # Get the sample sets for this release.
+                release_sample_sets_df = self.sample_sets(release=release)
+
+                # Only include if there are sample sets for this release.
+                if (
+                    release_sample_sets_df is not None
+                    and not release_sample_sets_df.empty
+                ):
+                    sample_set_dfs.append(release_sample_sets_df)
+
+            if sample_set_dfs:
+                # Concatenate the sample sets DataFrames from multiple releases.
+                df = pd.concat(sample_set_dfs, axis=0, ignore_index=True)
+            else:
+                # If there are no sample sets for this release, return an empty DataFrame.
+                df = pd.DataFrame()
 
         else:
             raise TypeError

malariagen_data/as1.py

@@ -0,0 +1,210 @@
+import sys
+
+import plotly.express as px  # type: ignore
+
+import malariagen_data
+from .anopheles import AnophelesDataResource
+
+MAJOR_VERSION_NUMBER = 1
+MAJOR_VERSION_PATH = "v1.0"
+CONFIG_PATH = "v1.0-config.json"
+GCS_DEFAULT_URL = "gs://vo_aste_release_master_us_central1/"
+GCS_DEFAULT_PUBLIC_URL = "gs://vo_aste_temp_us_central1/vo_aste_release/"
+GCS_REGION_URLS = {
+    "us-central1": "gs://vo_aste_release_master_us_central1",
+}
+XPEHH_GWSS_CACHE_NAME = "as1_xpehh_gwss_v1"
+IHS_GWSS_CACHE_NAME = "as1_ihs_gwss_v1"
+
+TAXON_PALETTE = px.colors.qualitative.Plotly
+TAXON_COLORS = {
+    "stephensi": TAXON_PALETTE[0],
+}
+
+
+class As1(AnophelesDataResource):
+    """Provides access to data from As1.x releases.
+
+    Parameters
+    ----------
+    url : str, optional
+        Base path to data. Defaults to use Google Cloud Storage, or can
+        be a local path on your file system if data have been downloaded.
+    site_filters_analysis : str, optional
+        Site filters analysis version.
+    bokeh_output_notebook : bool, optional
+        If True (default), configure bokeh to output plots to the notebook.
+    results_cache : str, optional
+        Path to directory on local file system to save results.
+    log : str or stream, optional
+        File path or stream output for logging messages.
+    debug : bool, optional
+        Set to True to enable debug level logging.
+    show_progress : bool, optional
+        If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS.
+    check_location : bool, optional
+        If True, use ipinfo to check the location of the client system.
+    **kwargs
+        Passed through to fsspec when setting up file system access.
+
+    Examples
+    --------
+    Access data from Google Cloud Storage (default):
+
+        >>> import malariagen_data
+        >>> as1 = malariagen_data.As1()
+
+    Access data downloaded to a local file system:
+
+        >>> as1 = malariagen_data.As1("/local/path/to/vo_aste_release/")
+
+    Access data from Google Cloud Storage, with caching on the local file system
+    in a directory named "gcs_cache":
+
+        >>> as1 = malariagen_data.As1(
+        ...     "simplecache::gs://vo_aste_release_master_us_central1",
+        ...     simplecache=dict(cache_storage="gcs_cache"),
+        ... )
+
+    Set up caching of some longer-running computations on the local file system,
+    in a directory named "results_cache":
+
+        >>> as1 = malariagen_data.As1(results_cache="results_cache")
+
+    """
+
+    _xpehh_gwss_cache_name = XPEHH_GWSS_CACHE_NAME
+    _ihs_gwss_cache_name = IHS_GWSS_CACHE_NAME
+
+    def __init__(
+        self,
+        url=None,
+        public_url=GCS_DEFAULT_PUBLIC_URL,
+        bokeh_output_notebook=True,
+        results_cache=None,
+        log=sys.stdout,
+        debug=False,
+        show_progress=None,
+        check_location=True,
+        cohorts_analysis=None,
+        site_filters_analysis=None,
+        discordant_read_calls_analysis=None,
+        pre=False,
+        tqdm_class=None,
+        **storage_options,  # used by fsspec via init_filesystem()
+    ):
+        super().__init__(
+            url=url,
+            public_url=public_url,
+            config_path=CONFIG_PATH,
+            cohorts_analysis=cohorts_analysis,
+            aim_analysis=None,
+            aim_metadata_dtype=None,
+            aim_ids=None,
+            aim_palettes=None,
+            site_filters_analysis=site_filters_analysis,
+            discordant_read_calls_analysis=discordant_read_calls_analysis,
+            default_site_mask="stephensi",
+            default_phasing_analysis="stephensi",
+            default_coverage_calls_analysis="stephensi",
+            bokeh_output_notebook=bokeh_output_notebook,
+            results_cache=results_cache,
+            log=log,
+            debug=debug,
+            show_progress=show_progress,
+            check_location=check_location,
+            pre=pre,
+            gcs_default_url=GCS_DEFAULT_URL,
+            gcs_region_urls=GCS_REGION_URLS,
+            major_version_number=MAJOR_VERSION_NUMBER,
+            major_version_path=MAJOR_VERSION_PATH,
+            gff_gene_type="protein_coding_gene",
+            gff_gene_name_attribute="Note",
+            gff_default_attributes=("ID", "Parent", "Note", "description"),
+            storage_options=storage_options,  # used by fsspec via init_filesystem()
+            tqdm_class=tqdm_class,
+            taxon_colors=TAXON_COLORS,
+            virtual_contigs=None,
+            gene_names=None,
+            inversion_tag_path=None,
+        )
+
+    def __repr__(self):
+        text = (
+            f"<MalariaGEN Af1 API client>\n"
+            f"Storage URL             : {self._url}\n"
+            f"Data releases available : {', '.join(self.releases)}\n"
+            f"Results cache           : {self._results_cache}\n"
+            f"Cohorts analysis        : {self._cohorts_analysis}\n"
+            f"Site filters analysis   : {self._site_filters_analysis}\n"
+            f"Software version        : malariagen_data {malariagen_data.__version__}\n"
+            f"Client location         : {self.client_location}\n"
+            f"---\n"
+            f"Please note that data are subject to terms of use,\n"
+            f"for more information see https://www.malariagen.net/data\n"
+            f"or contact support@malariagen.net. For API documentation see \n"
+            f"https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/As1.html"
+        )
+        return text
+
+    def _repr_html_(self):
+        html = f"""
+            <table class="malariagen-as1">
+                <thead>
+                    <tr>
+                        <th style="text-align: left" colspan="2">MalariaGEN As1 API client</th>
+                    </tr>
+                    <tr><td colspan="2" style="text-align: left">
+                        Please note that data are subject to terms of use,
+                        for more information see <a href="https://www.malariagen.net/data">
+                        the MalariaGEN website</a> or contact support@malariagen.net.
+                        See also the <a href="https://malariagen.github.io/malariagen-data-python/v{malariagen_data.__version__}/As1.html">As1 API docs</a>.
+                    </td></tr>
+                </thead>
+                <tbody>
+                    <tr>
+                        <th style="text-align: left">
+                            Storage URL
+                        </th>
+                        <td>{self._url}</td>
+                    </tr>
+                    <tr>
+                        <th style="text-align: left">
+                            Data releases available
+                        </th>
+                        <td>{', '.join(self.releases)}</td>
+                    </tr>
+                    <tr>
+                        <th style="text-align: left">
+                            Results cache
+                        </th>
+                        <td>{self._results_cache}</td>
+                    </tr>
+                    <tr>
+                        <th style="text-align: left">
+                            Cohorts analysis
+                        </th>
+                        <td>{self._cohorts_analysis}</td>
+                    </tr>
+                    <tr>
+                        <th style="text-align: left">
+                            Site filters analysis
+                        </th>
+                        <td>{self._site_filters_analysis}</td>
+                    </tr>
+                    <tr>
+                        <th style="text-align: left">
+                            Software version
+                        </th>
+                        <td>malariagen_data {malariagen_data.__version__}</td>
+                    </tr>
+                    <tr>
+                        <th style="text-align: left">
+                            Client location
+                        </th>
+                        <td>{self.client_location}</td>
+                    </tr>
+                </tbody>
+            </table>
+        """
+        return html

tests/integration/test_as1.py

@@ -0,0 +1,22 @@
+from malariagen_data import As1
+
+
+def setup_as1(url="simplecache::gs://vo_aste_release_master_us_central1/", **kwargs):
+    kwargs.setdefault("check_location", False)
+    kwargs.setdefault("show_progress", False)
+    if url is None:
+        # Test the default URL.
+        # Note: This only tests the setup_as1 default URL, not the As1 default.
+        # The test_anopheles setup_subclass tests the true defaults.
+        return As1(**kwargs)
+    if url.startswith("simplecache::"):
+        # Configure the directory on the local file system to cache data.
+        kwargs["simplecache"] = dict(cache_storage="gcs_cache")
+    return As1(url, **kwargs)
+
+
+def test_repr():
+    as1 = setup_as1(check_location=True)
+    assert isinstance(as1, As1)
+    r = repr(as1)
+    assert isinstance(r, str)