mgkit.snps.mapper module¶
Mapping functions for SNPs - Should be move into an ‘iterator’ package to be shared with other modules?
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mgkit.snps.mapper.
map_gene_id
(gene_id, gene_map=None)¶ Returns an iterator for all the values of a dictionary. if gene_id is not found in the gene_map, an empty iterator is returned.
Parameters: - gene_id (immutable) – gene_id or any other dictionary key.
- gene_map (dict) – a dictionary in the form key->[v1, v2, .. vN]
Returns: iterator (empty if gene_id is not in gene_map) with the values
Return type: generator
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mgkit.snps.mapper.
map_taxon_id_to_ancestor
(taxon_id, anc_ids=None, func=None)¶ Given a taxon_id and a list of ancestors IDs, returns an iterator with the IDs that are ancestors of taxon_id.
Parameters: - taxon_id (int) – taxon ID to be mapped
- anc_ids (iterable) – taxon IDs to check for ancestry
- func – function used to check for ancestry - partial function for
mgkit.taxon.is_ancestor()
that accepts taxon_id and anc_id
Returns: iterator with the values or empty
Return type: generator
Note
check
mgkit.filter.taxon.filter_taxon_by_id_list()
for examples on using func
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mgkit.snps.mapper.
map_taxon_id_to_rank
(taxon_id, rank=None, taxonomy=None, include_higher=False)¶ Given a taxon_id, returns an iterator with only the element that correspond to the requested rank. If the taxon returned by
mgkit.taxon.UniprotTaxonomy.get_ranked_taxon
has a different rank than requested, the iterator will be empty if include_higher is False and the returned taxon ID if True.Parameters: Returns: iterator with the values or empty
Return type: generator