Amin1 API
Contents
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