divbrowse.lib.variant_calls_slice¶
Module Contents¶
Classes¶
Functions¶
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- divbrowse.lib.variant_calls_slice.with_gd()¶
- class divbrowse.lib.variant_calls_slice.VariantCallsSlice¶
- gd :GenotypeData¶
- type_of_slice :str = range¶
- positional_lookup_success :bool = True¶
- sliced_variant_calls :numpy.ndarray¶
- positions :numpy.ndarray¶
- positions_indices :numpy.ndarray¶
- positions_not_found :numpy.ndarray¶
- location_start :int¶
- location_end :int¶
- samples_mask :numpy.ndarray¶
- samples_selected_mapped :list¶
- variant_filter_settings :dict¶
- calls_metadata :dict¶
- calc_summary_stats :bool = False¶
- __post_init__()¶
- static calculate_mean(slice_of_variant_calls: numpy.ndarray) numpy.ndarray¶
Calculate the mean for each variant of a variant matrix array holding the number of alternate alleles
Note
Missing variant calls are excluded from the mean calculation
- Parameters
slice_of_variant_calls (numpy.ndarray) – Numpy array representing a variant matrix holding the number of alternate allele calls
- Returns
Numpy array holding the means per variant
- Return type
numpy.ndarray
- count_alternate_alleles()¶
Returns a tupel consisting of a boolean mask for found sample Ids and a list of mapped sample IDs
- Parameters
sliced_variant_calls (numpy.ndarray) – variant matrix array holding the allele calls (0/0 0/1 1/1)
- Returns
variant matrix array holding the number of alternate allele calls
- Return type
numpy.ndarray
- calculate_minor_allele_freq()¶
Calculates minor allele frequency
- Returns
Numpy array (1d) holding the calculated minor allele frequencies per each variant
- Return type
numpy.ndarray
- calc_variants_summary_stats()¶
- calc_variants_summary_stats_numpy()¶
- calc_variants_summary_stats_scikitallel()¶
- apply_variant_filter_settings()¶
- add_stats()¶
- get_stats_dict()¶
- get_data()¶