mgkit.snps.filter module¶
SNPs filtering functions
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mgkit.snps.filter.
filter_genesyn_by_coverage
(gene_syn, min_cov=None)¶ Checks if the coverage of the provided gene_syn is at least min_cov
Parameters: - gene_syn –
GeneSyn
instance - min_cov (int) – minimum coverage allowed (included)
Returns: True if the gene has enough coverage
Return type: Raises: FilterFails
– if min_cov is None- gene_syn –
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mgkit.snps.filter.
filter_genesyn_by_gene_id
(gene_syn, gene_ids=None, exclude=False, id_func=None)¶ Checks if the gene_id is listed in the filter_list.
Parameters: - gene_syn –
GeneSyn
instance - gene_ids (iterable) – list of gene IDs to include/exclude
- exclude (bool) – if the filter is reversed
Returns: if the exclude is True, the gene_id must appear in the gene_ids, if False, returns True only if gene_id is NOT in gene_ids.
Return type: Raises: FilterFails
– if gene_ids is None- gene_syn –
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mgkit.snps.filter.
filter_genesyn_by_taxon_id
(gene_syn, taxonomy=None, filter_list=None, exclude=False, func=None)¶ Checks if the taxon_id attribute of gene_syn is the filter_list. Excelude reverses the result. If func is supplied, it’s used to traverse the taxonomy.
Parameters: - gene_syn –
GeneSyn
instance - taxonomy – a valid taxonomy (instance of
UniprotTaxonomy
) - filter_list (iterable) – list of taxon IDs to include/exclude
- exclude (bool) – if the filter is reversed
- func (func) –
is_ancestor()
Returns: if the exclude is True, the gene_id must appear in the gene_ids, if False, returns True only if gene_id is NOT in gene_ids.
Return type: Raises: FilterFails
– if filter_list is None or taxonomy is None and func is not None- gene_syn –
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mgkit.snps.filter.
get_default_filters
(taxonomy, **kwargs)¶ Retuns a list of filters that are used by default. it needs a valid taxonomy and gets the default arguments from
mgkit.consts.DEFAULT_SNP_FILTER
.
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mgkit.snps.filter.
pipe_filters
(iterable, *funcs)¶ Pipes a list of filter to iterable, using the python ifilter function in the itertools module.