capalyzer.packet_parser package
Submodules
capalyzer.packet_parser.cli module
capalyzer.packet_parser.dataframes module
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class
capalyzer.packet_parser.dataframes.DataTableFactory(packet_dir, metadata_tbl=None)[source]
Bases: object
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ags(**kwargs)[source]
Return a Series of Ave Genome Size estimates.
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alpha_diversity(tbl, **kwargs)[source]
Return generic alpha diversity table.
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amr_alpha_diversity(**kwargs)[source]
Return a Series of diversities.
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amr_beta_diversity(**kwargs)[source]
Return a distance matrix between taxa.
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amr_rarefaction(**kwargs)[source]
Return a rarefaction analysis of taxa.
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amrs(**kwargs)[source]
Return an AMR table.
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beta_diversity(tbl, **kwargs)[source]
Return generic beta diversity table.
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copy(new_metadata=None)[source]
Return a deep copy, with a new metadata table. if specified
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core_taxa(core_thresh=0.9, pan_thresh=0.2, zero_thresh=0, **kwargs)[source]
Return a pandas dataframe grouping taxa into core, pan, and peripheral.
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csv_in_dir(fname, **kwargs)[source]
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filter_dataframe(tbl, **kwargs)[source]
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hmp(**kwargs)[source]
Return a table of HMP distances.
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macrobes(**kwargs)[source]
Return a table of macrobe abundances.
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pathways(coverage_min=0, **kwargs)[source]
Return a table of pathways.
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rarefaction(tbl, **kwargs)[source]
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read_props(**kwargs)[source]
Return a table of the proportion of reads assigned to macro categories.
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read_stats(**kwargs)[source]
Return a table of the gc content and reads counts.
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set_metadata(metadata_tbl)[source]
Set the internal metadata table which will be used to filter samples in tables.
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taxa_alpha_diversity(**kwargs)[source]
Return a Series of diversities.
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taxa_beta_diversity(**kwargs)[source]
Return a distance matrix between taxa.
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taxa_rarefaction(**kwargs)[source]
Return a rarefaction analysis of taxa.
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taxonomy(**kwargs)[source]
Return a taxonomy table.
capalyzer.packet_parser.diversity_metrics module
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capalyzer.packet_parser.diversity_metrics.chao1(row, rarefy=0)[source]
Return richnes of an iterable
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capalyzer.packet_parser.diversity_metrics.clr(X)[source]
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capalyzer.packet_parser.diversity_metrics.jensen_shannon_dist(P, Q)[source]
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capalyzer.packet_parser.diversity_metrics.random() → x in the interval [0, 1).
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capalyzer.packet_parser.diversity_metrics.rarefaction_analysis(tbl, ns=[], nsample=16, include_all=True)[source]
Return a dataframe with two columns.
N, the number of samples and Taxa, the number of nonzero elements.
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capalyzer.packet_parser.diversity_metrics.rho_proportionality(P, Q)[source]
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capalyzer.packet_parser.diversity_metrics.richness(row, rarefy=0, count=False)[source]
Return the richness of an iterable.
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capalyzer.packet_parser.diversity_metrics.shannon_entropy(row, rarefy=0)[source]
Return the shannon entropy of an iterable.
Shannon entropy is robust to rarefaction but we keep
the param for consistency.
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capalyzer.packet_parser.diversity_metrics.single_rarefaction(tbl, n=0)[source]
Return the number of nonzero columns in tbl.
Select n rows at random if specified.
capalyzer.packet_parser.taxa_tree module
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class
capalyzer.packet_parser.taxa_tree.NCBITaxaTree(parent_map, names_to_nodes, nodes_to_name)[source]
Bases: object
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ancestor_rank(rank, taxon, default=None)[source]
Return the ancestor of taxon at the given rank.
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ancestors(taxon)[source]
Return a list of all ancestors of the taxon starting with the taxon itself.
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genus(taxon, default=None)[source]
Return the genus for the given taxon.
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parent(taxon)[source]
Return the name of the parent taxon.
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classmethod
parse_files(names_filename=None, nodes_filename=None)[source]
Return a tree parsed from the given files.
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phyla(taxon, default=None)[source]
Return the phyla for the given taxon.
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rank(taxon)[source]
Return the rank of the given taxon.
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ranked_ancestors(taxon)[source]
Return a dict of all ancestors of the taxon starting with the taxon itself.
Keys of the dict are taxon ranks
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taxa_sort(taxa)[source]
Return a list with all elements of taxa in DFS order.
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class
capalyzer.packet_parser.taxa_tree.TaxaTree(taxa, ncbi_tree=None)[source]
Bases: object
Represent a taxa tree for a specific set of taxa.
Uses the NCBI taxonomy.
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to_newick()[source]
Return a newick string corresponding to this tree.
Module contents