Region of the reference genome. Can be a contig name, region string
+(formatted like “{contig}:{start}-{end}”), or identifier of a genome
+feature such as a gene or transcript.
+
+
cohortsstr or Mapping[str, str]
Either a string giving the name of a predefined cohort set (e.g.,
+“admin1_month”) or a dict mapping custom cohort labels to sample
+queries.
+
+
sample_querystr or None, optional
A pandas query string to be evaluated against the sample metadata, to
+select samples to be included in the returned data.
+
+
sample_query_optionsdict or None, optional
A dictionary of arguments that will be passed through to pandas
+query() or eval(), e.g. parser, engine, local_dict, global_dict,
+resolvers.
+
+
min_cohort_sizeint, optional, default: 10
Minimum cohort size. Raise an error if the number of samples is less
+than this value.
+
+
sample_setssequence of str or str or None, optional
List of sample sets and/or releases. Can also be a single sample set
+or release.
+
+
chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘native’
Define how input data being read from zarr should be divided into
+chunks for a dask computation. If ‘native’, use underlying zarr
+chunks. If a string specifying a target memory size, e.g., ‘300 MiB’,
+resize chunks in arrays with more than one dimension to match this
+size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask
+decide chunk size but only for arrays with more than one dimension. If
+‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If
+‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If
+‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk
+dimensions. Also, can be a tuple of integers, or a callable which
+accepts the native chunks as a single argument and returns a valid
+dask chunks value.
Region of the reference genome. Can be a contig name, region string
+(formatted like “{contig}:{start}-{end}”), or identifier of a genome
+feature such as a gene or transcript.
+
+
area_bystr
Column name in the sample metadata to use to group samples spatially.
+E.g., use “admin1_iso” or “admin1_name” to group by level 1
+administrative divisions, or use “admin2_name” to group by level 2
+administrative divisions.
+
+
period_by{‘year’, ‘quarter’, ‘month’}
Length of time to group samples temporally.
+
+
sample_setssequence of str or str or None, optional
List of sample sets and/or releases. Can also be a single sample set
+or release.
+
+
sample_querystr or None, optional
A pandas query string to be evaluated against the sample metadata, to
+select samples to be included in the returned data.
+
+
sample_query_optionsdict or None, optional
A dictionary of arguments that will be passed through to pandas
+query() or eval(), e.g. parser, engine, local_dict, global_dict,
+resolvers.
+
+
min_cohort_sizeint, optional, default: 10
Minimum cohort size. Raise an error if the number of samples is less
+than this value.
+
+
ci_method{‘normal’, ‘agresti_coull’, ‘beta’, ‘wilson’, ‘binom_test’} or None, optional, default: ‘wilson’
Method to use for computing confidence intervals, passed through to
+statsmodels.stats.proportion.proportion_confint.
+
+
chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘native’
Define how input data being read from zarr should be divided into
+chunks for a dask computation. If ‘native’, use underlying zarr
+chunks. If a string specifying a target memory size, e.g., ‘300 MiB’,
+resize chunks in arrays with more than one dimension to match this
+size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask
+decide chunk size but only for arrays with more than one dimension. If
+‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If
+‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If
+‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk
+dimensions. Also, can be a tuple of integers, or a callable which
+accepts the native chunks as a single argument and returns a valid
+dask chunks value.
The resulting dataset contains data has dimensions “cohorts” and
+“variants”. Variables prefixed with “cohort” are 1-dimensional
+arrays with data about the cohorts, such as the area, period, taxon
+and cohort size. Variables prefixed with “variant” are 1-dimensional
+arrays with data about the variants, such as the contig, position,
+reference and alternate alleles. Variables prefixed with “event” are
+2-dimensional arrays with the allele counts and frequency
+calculations.
Region of the reference genome. Can be a contig name, region string
+(formatted like “{contig}:{start}-{end}”), or identifier of a genome
+feature such as a gene or transcript.
+
+
cohortsstr or Mapping[str, str]
Either a string giving the name of a predefined cohort set (e.g.,
+“admin1_month”) or a dict mapping custom cohort labels to sample
+queries.
+
+
sample_querystr or None, optional
A pandas query string to be evaluated against the sample metadata, to
+select samples to be included in the returned data.
+
+
sample_query_optionsdict or None, optional
A dictionary of arguments that will be passed through to pandas
+query() or eval(), e.g. parser, engine, local_dict, global_dict,
+resolvers.
+
+
min_cohort_sizeint, optional, default: 10
Minimum cohort size. Raise an error if the number of samples is less
+than this value.
+
+
sample_setssequence of str or str or None, optional
List of sample sets and/or releases. Can also be a single sample set
+or release.
+
+
chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘native’
Define how input data being read from zarr should be divided into
+chunks for a dask computation. If ‘native’, use underlying zarr
+chunks. If a string specifying a target memory size, e.g., ‘300 MiB’,
+resize chunks in arrays with more than one dimension to match this
+size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask
+decide chunk size but only for arrays with more than one dimension. If
+‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If
+‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If
+‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk
+dimensions. Also, can be a tuple of integers, or a callable which
+accepts the native chunks as a single argument and returns a valid
+dask chunks value.
Region of the reference genome. Can be a contig name, region string
+(formatted like “{contig}:{start}-{end}”), or identifier of a genome
+feature such as a gene or transcript.
+
+
area_bystr
Column name in the sample metadata to use to group samples spatially.
+E.g., use “admin1_iso” or “admin1_name” to group by level 1
+administrative divisions, or use “admin2_name” to group by level 2
+administrative divisions.
+
+
period_by{‘year’, ‘quarter’, ‘month’}
Length of time to group samples temporally.
+
+
sample_setssequence of str or str or None, optional
List of sample sets and/or releases. Can also be a single sample set
+or release.
+
+
sample_querystr or None, optional
A pandas query string to be evaluated against the sample metadata, to
+select samples to be included in the returned data.
+
+
sample_query_optionsdict or None, optional
A dictionary of arguments that will be passed through to pandas
+query() or eval(), e.g. parser, engine, local_dict, global_dict,
+resolvers.
+
+
min_cohort_sizeint, optional, default: 10
Minimum cohort size. Raise an error if the number of samples is less
+than this value.
+
+
ci_method{‘normal’, ‘agresti_coull’, ‘beta’, ‘wilson’, ‘binom_test’} or None, optional, default: ‘wilson’
Method to use for computing confidence intervals, passed through to
+statsmodels.stats.proportion.proportion_confint.
+
+
chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘native’
Define how input data being read from zarr should be divided into
+chunks for a dask computation. If ‘native’, use underlying zarr
+chunks. If a string specifying a target memory size, e.g., ‘300 MiB’,
+resize chunks in arrays with more than one dimension to match this
+size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask
+decide chunk size but only for arrays with more than one dimension. If
+‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If
+‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If
+‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk
+dimensions. Also, can be a tuple of integers, or a callable which
+accepts the native chunks as a single argument and returns a valid
+dask chunks value.
The resulting dataset contains data has dimensions “cohorts” and
+“variants”. Variables prefixed with “cohort” are 1-dimensional
+arrays with data about the cohorts, such as the area, period, taxon
+and cohort size. Variables prefixed with “variant” are 1-dimensional
+arrays with data about the variants, such as the contig, position,
+reference and alternate alleles. Variables prefixed with “event” are
+2-dimensional arrays with the allele counts and frequency
+calculations.
+