gnomad.utils.release

gnomad.utils.release.make_faf_index_dict(...)

Create a look-up Dictionary for entries contained in the filter allele frequency annotation array.

gnomad.utils.release.make_freq_index_dict(...)

Create a look-up Dictionary for entries contained in the frequency annotation array.

gnomad.utils.release.make_freq_index_dict_from_meta(...)

Create a dictionary for accessing frequency array.
gnomad.utils.release.make_faf_index_dict(faf_meta, groups=['adj'], pops=['afr', 'amr', 'asj', 'eas', 'fin', 'mid', 'nfe', 'remaining', 'sas'], sexes=['XX', 'XY'], label_delimiter='_')[source]

Create a look-up Dictionary for entries contained in the filter allele frequency annotation array.

Parameters:

  • faf_meta (List[Dict[str, str]]) – Global annotation containing the set of groupings for each element of the faf array (e.g., [{‘group’: ‘adj’}, {‘group’: ‘adj’, ‘pop’: ‘nfe’}])

  • groups (List[str]) – List of sample groups [adj, raw]. Default is GROUPS

  • pops (List[str]) – List of sample global population names for gnomAD data type. Default is POPS[CURRENT_MAJOR_RELEASE][“exomes”].

  • sexes (List[str]) – List of sample sexes used in VCF export. Default is SEXES

  • label_delimiter (str) – String used as delimiter when making group label combinations

Return type:

Dict[str, int]

Returns:

Dictionary of faf annotation population groupings, where values are the corresponding 0-based indices for the groupings in the faf_meta array

gnomad.utils.release.make_freq_index_dict(freq_meta, groups=['adj', 'raw'], pops=['afr', 'amr', 'asj', 'eas', 'fin', 'mid', 'nfe', 'remaining', 'sas'], sexes=['XX', 'XY'], subsets=['non_ukb'], downsamplings=None, label_delimiter='_')[source]

Create a look-up Dictionary for entries contained in the frequency annotation array.

Parameters:

  • freq_meta (List[Dict[str, str]]) – List containing the set of groupings for each element of the freq array (e.g., [{‘group’: ‘adj’}, {‘group’: ‘adj’, ‘pop’: ‘nfe’}])

  • groups (List[str]) – List of sample groups [adj, raw]. Default is GROUPS

  • pops (List[str]) – List of sample global population names for gnomAD data type. Default is POPS[CURRENT_MAJOR_RELEASE][“exomes”].

  • sexes (List[str]) – List of sample sexes used in VCF export. Default is SEXES

  • subsets (List[str]) – List of sample subsets in dataset. Default is SUBSETS[CURRENT_MAJOR_RELEASE]

  • downsamplings (Optional[List[int]]) – List of downsampling cohort sizes present in global frequency array

  • label_delimiter (str) – String used as delimiter when making group label combinations

Return type:

Dict[str, int]

Returns:

Dictionary keyed by the grouping combinations found in the frequency array, where values are the corresponding 0-based indices for the groupings in the freq_meta array

gnomad.utils.release.make_freq_index_dict_from_meta(freq_meta, label_delimiter='_', sort_order=['subset', 'downsampling', 'popmax', 'grpmax', 'pop', 'gen_anc', 'subpop', 'sex', 'group'])[source]

Create a dictionary for accessing frequency array.

The dictionary is keyed by the grouping combinations found in the frequency metadata array, where values are the corresponding 0-based indices for the groupings in the frequency array. For example, if the freq_meta entry [{‘pop’: ‘nfe’}, {‘sex’: ‘XX’}] corresponds to the 5th entry in the frequency array, the returned dictionary entry would be {‘nfe_XX’: 4}.

Parameters:

  • freq_meta (List[Dict[str, str]]) – List of dictionaries containing frequency metadata.

  • label_delimiter (str) – Delimiter to use when joining frequency metadata labels.

  • sort_order (Optional[List[str]]) – List of frequency metadata labels to use when sorting the dictionary.

Return type:

Dict[str, int]

Returns:

Dictionary of frequency metadata.