mgkit.snps.conv_func module¶
Wappers to use some of the general function of the snps package in a simpler way.
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mgkit.snps.conv_func.
get_full_dataframe
(snp_data, taxonomy, min_num=3, index_type=None, filters=None)[source]¶ New in version 0.1.12.
Changed in version 0.2.2: added filters argument
Returns a
DataFrame
with the pN/pS of the given SNPs data.Shortcut for using
combine_sample_snps()
, using filters fromget_default_filters()
.Parameters: Returns: pandas.DataFrame
of pN/pS values. The index type is None (gene-taxon)Return type: DataFrame
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mgkit.snps.conv_func.
get_gene_map_dataframe
(snp_data, taxonomy, gene_map, min_num=3, index_type='gene', filters=None)[source]¶ New in version 0.1.11.
Changed in version 0.2.2: added filters argument
Returns a
DataFrame
with the pN/pS of the given SNPs data, mapping all taxa to the gene map.Shortcut for using
combine_sample_snps()
, using filters fromget_default_filters()
and as gene_func parametermap_gene_id()
.Parameters: - snp_data (dict) – dictionary sample->GeneSyn of SNPs data
- taxonomy – Uniprot Taxonomy
- min_num (int) – minimum number of samples in which a valid pN/pS is found
- gene_map (dict) – dictionary of mapping for the gene_ids in in SNPs data
- index_type (str, None) – type of index to return
- filters (iterable) – list of filters to apply, otherwise uses the default filters
Returns: pandas.DataFrame
of pN/pS values. The index type is ‘gene’Return type: DataFrame
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mgkit.snps.conv_func.
get_gene_taxon_dataframe
(snp_data, taxonomy, gene_map, min_num=3, rank='genus', index_type=None, filters=None)[source]¶ New in version 0.1.12.
Changed in version 0.2.2: added filters argument
Todo
edit docstring
Returns a
DataFrame
with the pN/pS of the given SNPs data, mapping all taxa to the gene map.Shortcut for using
combine_sample_snps()
, using filters fromget_default_filters()
and as gene_func parametermap_gene_id()
.Parameters: - snp_data (dict) – dictionary sample->GeneSyn of SNPs data
- taxonomy – Uniprot Taxonomy
- min_num (int) – minimum number of samples in which a valid pN/pS is found
- gene_map (dict) – dictionary of mapping for the gene_ids in in SNPs data
- index_type (str, None) – type of index to return
- filters (iterable) – list of filters to apply, otherwise uses the default filters
Returns: pandas.DataFrame
of pN/pS values. The index type is ‘gene’Return type: DataFrame
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mgkit.snps.conv_func.
get_rank_dataframe
(snp_data, taxonomy, min_num=3, rank='order', index_type='taxon', filters=None)[source]¶ New in version 0.1.11.
Changed in version 0.2.2: added filters argument
Returns a
DataFrame
with the pN/pS of the given SNPs data, mapping all taxa to the specified rank. Higher taxa won’t be included.Shortcut for using
combine_sample_snps()
, using filters fromget_default_filters()
and as taxon_func parametermap_taxon_id_to_rank()
, with include_higher equals to FalseParameters: - snp_data (dict) – dictionary sample->GeneSyn of SNPs data
- taxonomy – Uniprot Taxonomy
- min_num (int) – minimum number of samples in which a valid pN/pS is found
- rank (str) – taxon rank to map. Valid ranks are found in
mgkit.taxon.TAXON_RANKS
- index_type (str, None) – type of index to return
- filters (iterable) – list of filters to apply, otherwise uses the default filters
Returns: pandas.DataFrame
of pN/pS values. The index type is ‘taxon’Return type: DataFrame