Amin1 API#

This page provides documentation for functions in the malariagen_data Python package for accessing Anopheles minimus data.

Amin1()#

malariagen_data.Amin1(**kwargs)#

sample_metadata()#

Amin1.sample_metadata()#

Access sample metadata.

Returns
dfpandas.DataFrame

genome_sequence()#

Amin1.genome_sequence(region, inline_array=True, chunks='native')#

Access the reference genome sequence.

Parameters
region: str or list of str or Region

Contig (e.g., “KB663610”), gene name (e.g., “AMIN002150”), genomic region defined with coordinates (e.g., “KB663610:1-100000”) or a named tuple with genomic location Region(contig, start, end). Multiple values can be provided as a list, in which case data will be concatenated.

inline_arraybool, optional

Passed through to dask.array.from_array().

chunksstr, optional

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also can be a target size, e.g., ‘200 MiB’.

Returns
ddask.array.Array

geneset()#

Amin1.geneset(*args, **kwargs)#

Deprecated, this method has been renamed to genome_features().

snp_calls()#

Amin1.snp_calls(region, site_mask=False, inline_array=True, chunks='native')#

Access SNP sites, site filters and genotype calls.

Parameters
region: str or list of str or Region

Contig (e.g., “KB663610”), gene name (e.g., “AMIN002150”), genomic region defined with coordinates (e.g., “KB663610:1-100000”) or a named tuple with genomic location Region(contig, start, end). Multiple values can be provided as a list, in which case data will be concatenated.

site_maskbool

Apply site filters.

inline_arraybool, optional

Passed through to dask.array.from_array().

chunksstr, optional

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also can be a target size, e.g., ‘200 MiB’.

Returns
dsxarray.Dataset