Ag3 API

This page provides a curated list of functions and properties available in the malariagen_data API relating to Anopheles gambiae data.

Basic data access

client_location
config
lookup_release(sample_set)	Find which release a sample set was included in.
open_file(path)
read_files(paths[, on_error])
releases
results_cache_get(*, name, params)
results_cache_set(*, name, params, results)
sample_sets([release])	Access a dataframe of sample sets.

Sample metadata access

add_extra_metadata(data[, on])	Add extra sample metadata, e.g., including additional columns which you would like to use to query and group samples.
aim_metadata([sample_sets])	Access ancestry-informative marker (AIM) metadata for one or more sample sets.
clear_extra_metadata()	Clear any extra metadata previously added.
cohorts_metadata([sample_sets])	Access cohort membership metadata for one or more sample sets.
count_samples([sample_sets, sample_query, ...])	Create a pivot table showing numbers of samples available by space, time and taxon.
general_metadata([sample_sets])	Read general sample metadata for one or more sample sets into a pandas DataFrame.
lookup_sample(sample[, sample_set])	Get the metadata for a specific sample and sample set.
plot_samples_bar(x[, color, sort, ...])	Plot a bar chart showing the number of samples available, grouped by some variable such as country or year.
plot_samples_interactive_map([sample_sets, ...])	Plot an interactive map showing sampling locations using ipyleaflet.
sample_metadata([sample_sets, sample_query, ...])	Access sample metadata for one or more sample sets.
wgs_data_catalog(sample_set)	Load a data catalog providing URLs for downloading BAM, VCF and Zarr files for samples in a given sample set.

SNP data access

is_accessible(region[, site_mask, ...])	Compute genome accessibility array.
open_site_annotations()	Open site annotations zarr.
open_site_filters(mask)	Open site filters zarr.
open_snp_genotypes(sample_set)	Open SNP genotypes zarr for a given sample set.
open_snp_sites()	Open SNP sites zarr.
plot_snps(region[, sample_sets, ...])	Plot SNPs in a given genome region.
plot_snps_track(region[, sample_sets, ...])	Plot SNPs in a given genome region.
site_annotations(region[, site_mask, ...])	Load site annotations.
site_filters(region, mask[, field, ...])	Access SNP site filters.
site_mask_ids	Identifiers for the different site masks that are available.
snp_allele_counts(region[, sample_sets, ...])	Compute SNP allele counts.
snp_calls(region[, sample_sets, ...])	Access SNP sites, site filters and genotype calls.
snp_dataset(*args, **kwargs)	Deprecated, this method has been renamed to snp_calls().
snp_genotypes(region[, sample_sets, ...])	Access SNP genotypes and associated data.
snp_sites(region, field[, site_mask, ...])	Access SNP site data (positions or alleles).
snp_variants(region[, site_mask, ...])	Access SNP sites and site filters.

Haplotype data access

haplotypes(region[, analysis, sample_sets, ...])	Access haplotype data.
open_haplotypes(sample_set[, analysis])	Open haplotypes zarr.
open_haplotype_sites([analysis])	Open haplotype sites zarr.
phasing_analysis_ids	Identifiers for the different phasing analyses that are available.

CNV data access

coverage_calls_analysis_ids	Identifiers for the different coverage calls analyses that are available.
cnv_coverage_calls(region, sample_set, analysis)	Access CNV HMM data from genome-wide CNV discovery and filtering.
cnv_discordant_read_calls(contig[, ...])	Access CNV discordant read calls data.
cnv_hmm(region[, sample_sets, sample_query, ...])	Access CNV HMM data from CNV calling.
open_cnv_coverage_calls(sample_set, analysis)	Open CNV coverage calls zarr.
open_cnv_discordant_read_calls(sample_set)	Open CNV discordant read calls zarr.
open_cnv_hmm(sample_set)	Open CNV HMM zarr.
plot_cnv_hmm_coverage(sample, region[, ...])	Plot CNV HMM data for a single sample, together with a genes track, using bokeh.
plot_cnv_hmm_coverage_track(sample, region)	Plot CNV HMM data for a single sample, using bokeh.
plot_cnv_hmm_heatmap(region[, sample_sets, ...])	Plot CNV HMM data for multiple samples as a heatmap, with a genes track, using bokeh.
plot_cnv_hmm_heatmap_track(region[, ...])	Plot CNV HMM data for multiple samples as a heatmap, using bokeh.