Merge pull request #1257 from tristanpwdennis/add-As1

Add As1 support

Author: tristanpwdennis

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/_static/images/anopheles_stephensi.jpg

@@ -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

docs/source/index.rst

@@ -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