Add As1 support

README.md

@@ -1,89 +1,15 @@
-# `malariagen_data` - analyse MalariaGEN data from Python
+# Curation metadata
 
-This Python package provides methods for accessing and analysing data from MalariaGEN.
+Summary statistics used during our sequence QC process are available within each sample set subdirectory, in a file named "sequence_qc_stats.csv". Each file contains the following fields:
 
-## Installation
+- `sample_id` (string) - MalariaGEN sample identifier
+- `mean_cov` (float) - mean coverage
+- `median_cov` (int) - median coverage
+- `modal_cov` (int) - modal coverage
+- `mean_cov_{contig}` (float) - mean coverage for a particular contig
+- `median_cov_{contig}` (int) - median coverage for a particular contig
+- `mode_cov_{contig}` (int) - modal coverage for a particular contig
+- `frac_gen_cov` (float) - fraction of the genome covered
+- `divergence` (float) - divergence
 
-The `malariagen_data` Python package is available from the Python
-package index (PyPI) and can be installed via `pip`, e.g.:
-
-```bash
-pip install malariagen-data
-```
-
-## Documentation
-
-Documentation of classes and methods in the public API are available
-from the following locations:
-
--   [Ag3 API
-    docs](https://malariagen.github.io/malariagen-data-python/latest/Ag3.html)
-
--   [Af1 API
-    docs](https://malariagen.github.io/malariagen-data-python/latest/Af1.html)
-
--   [Amin1 API
-    docs](https://malariagen.github.io/malariagen-data-python/latest/Amin1.html)
-
--  [Adir1 API
-    docs](https://malariagen.github.io/malariagen-data-python/latest/Adir1.html)
-
--   [Pf8 API
-    docs](https://malariagen.github.io/parasite-data/pf8/api.html)
-
--   [Pf7 API
-    docs](https://malariagen.github.io/parasite-data/pf7/api.html)
-
--   [Pv4 API
-    docs](https://malariagen.github.io/parasite-data/pv4/api.html)
-
-## Release notes (change log)
-
-See [GitHub releases](https://github.com/malariagen/malariagen-data-python/releases)
-for release notes.
-
-## Developer setup
-
-To get setup for development, see [this video if you prefer VS Code](https://youtu.be/zddl3n1DCFM), or [this older video if you prefer PyCharm](https://youtu.be/QniQi-Hoo9A).
-
-For detailed setup instructions, see:
-- [Linux setup guide](LINUX_SETUP.md)
-- [macOS setup guide](MACOS_SETUP.md)
-- [Windows setup guide](WINDOWS_SETUP.md)
-- [Google Colab (TPU) setup guide](docs/source/colab_tpu_runtime.rst)
-Detailed instructions can be found in the [Contributors guide](https://github.com/malariagen/malariagen-data-python/blob/master/CONTRIBUTING.md).
-
-## AI use policy and guidelines
-
-See [AI use policy and guidelines](https://github.com/malariagen/malariagen-data-python/blob/master/AI-POLICY.md) for more details.
-
-## Release process
-
-Create a new GitHub release. That's it. This will automatically
-trigger publishing of a new release to PyPI and a new version of
-the documentation via GitHub Actions.
-
-The version switcher for the documentation can then be updated by
-modifying the `docs/source/_static/switcher.json` file accordingly.
-
-## Citation
-
-If you use the `malariagen_data` package in a publication
-or include any of its functions or code in other materials (_e.g._ training resources),
-please cite: [doi.org/10.5281/zenodo.11173411](https://doi.org/10.5281/zenodo.11173411)
-
-Some functions may require additional citations to acknowledge specific contributions. These are indicated in the description for each relevant function.
-
-For any questions, please feel free to contact us at: [support@malariagen.net](mailto:support@malariagen.net)
-
-
-## Sponsorship
-
-This project is currently supported by the following grants:
-
-* [BMGF INV-068808](https://www.gatesfoundation.org/about/committed-grants/2024/04/inv-068808)
-* [BMGF INV-062921](https://www.gatesfoundation.org/about/committed-grants/2024/07/inv-062921)
-
-This project was previously supported by the following grants:
-
-* [BMGF INV-001927](https://www.gatesfoundation.org/about/committed-grants/2019/11/inv001927)
+For further information or queries contact support@malariagen.net.

docs/source/As1.rst

@@ -0,0 +1,141 @@
+As1
+=====
+
+This page provides a curated list of functions and properties available in the ``malariagen_data`` API
+for data on *Anopheles stephensi* species mosquitoes.
+
+To set up the API, use the following code::
+
+    import malariagen_data
+    as1 = malariagen_data.As1()
+
+All the functions below can then be accessed as methods on the ``as1`` object. E.g., to call the
+``sample_metadata()`` function, do::
+
+    df_samples = as1.sample_metadata()
+
+For more information about the data and terms of use, please see the
+`MalariaGEN website <https://www.malariagen.net/data>`_ or contact support@malariagen.net.
+
+.. currentmodule:: malariagen_data.as1.As1
+
+Basic data access
+-----------------
+.. autosummary::
+    :toctree: generated/
+
+    releases
+    sample_sets
+    lookup_release
+    lookup_study
+
+Reference genome data access
+----------------------------
+.. autosummary::
+    :toctree: generated/
+
+    contigs
+    genome_sequence
+    genome_features
+    plot_transcript
+    plot_genes
+
+Sample metadata access
+----------------------
+.. autosummary::
+    :toctree: generated/
+
+    sample_metadata
+    add_extra_metadata
+    clear_extra_metadata
+    lookup_sample
+    count_samples
+    plot_samples_bar
+    plot_samples_interactive_map
+    plot_sample_location_mapbox
+    plot_sample_location_geo
+    wgs_data_catalog
+    cohorts
+
+SNP data access
+---------------
+.. autosummary::
+    :toctree: generated/
+
+    site_mask_ids
+    snp_calls
+    snp_allele_counts
+    plot_snps
+    site_annotations
+    is_accessible
+    biallelic_snp_calls
+    biallelic_diplotypes
+    biallelic_snps_to_plink
+
+SNP frequency analysis
+----------------------
+.. autosummary::
+    :toctree: generated/
+
+    snp_allele_frequencies
+    snp_allele_frequencies_advanced
+    aa_allele_frequencies
+    aa_allele_frequencies_advanced
+    plot_frequencies_heatmap
+    plot_frequencies_time_series
+    plot_frequencies_interactive_map
+
+Principal components analysis (PCA)
+-----------------------------------
+.. autosummary::
+    :toctree: generated/
+
+    pca
+    plot_pca_variance
+    plot_pca_coords
+    plot_pca_coords_3d
+
+Genetic distance and neighbour-joining trees (NJT)
+--------------------------------------------------
+.. autosummary::
+    :toctree: generated/
+
+    plot_njt
+    njt
+    biallelic_diplotype_pairwise_distances
+
+Heterozygosity analysis
+-----------------------
+.. autosummary::
+    :toctree: generated/
+
+    plot_heterozygosity
+    roh_hmm
+    plot_roh
+
+Diversity analysis
+------------------
+.. autosummary::
+    :toctree: generated/
+
+    cohort_diversity_stats
+    diversity_stats
+    plot_diversity_stats
+
+Diplotype clustering
+--------------------
+.. autosummary::
+    :toctree: generated/
+
+    plot_diplotype_clustering
+
+Fst analysis
+------------
+.. autosummary::
+    :toctree: generated/
+
+    average_fst
+    pairwise_average_fst
+    plot_pairwise_average_fst
+    fst_gwss
+    plot_fst_gwss

docs/source/index.rst

@@ -33,6 +33,17 @@ API documentation
          :align: center
          :width: 100%
 
+   .. grid-item-card:: ``As1``
+      :link: As1
+      :link-type: doc
+
+      *Anopheles stephensi*.
+
+      .. image:: ./_static/images/anopheles_stephensi.jpg
+         :alt: Anopheles stephensi mosquito mosquito
+         :align: center
+         :width: 100%
+
    .. grid-item-card:: ``Amin1``
       :link: Amin1
       :link-type: doc

malariagen_data/__init__.py

@@ -4,6 +4,7 @@
 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