microbetag.pathway_complementarity

This script aims at calculating and exporting patwhay complementarities in case of running microbetag locally, with user-provided genomes.

Attributes

logger

Functions

build_kegg_url(kegg_map, clean_path, missing_kos[, ...])	Build url to colorify the related to the module kegg map based on the KO terms
all_alternatives(bin_kos_per_module, ...)	Build the alts.json file
all_complements(bin_kos_per_module, bins_alternatives, ...)	Extract potential complementarities from other bins
a_modules_maps(kegg_modules_to_maps)	Get the KEGG maps in which a module takes part in
taxon_kos_per_module(bins_kos_df, ref_ko_per_module)	Keep track of the KOs related to a module present on each bin
export_pathway_complementarities(config, bins_kos_df)	Function to get all the KEGG pathway complements among a set of bins

Module Contents

microbetag.pathway_complementarity.logger

microbetag.pathway_complementarity.build_kegg_url(kegg_map, clean_path, missing_kos, shortener=None)

Build url to colorify the related to the module kegg map based on the KO terms of the beneficiary (pink) and those it gets from the donor (green)

microbetag.pathway_complementarity.all_alternatives(bin_kos_per_module, modules_definitions_json_map, alts_output_file)

Build the alts.json file list alternatives for a bin’s modules to be completed

Inputs:

bin_kos_per_module (Dict): modules_definitions_json_map (str): path to

microbetag.pathway_complementarity.all_complements(bin_kos_per_module, bins_alternatives, module_to_map, compl_output_file, tinyurl=False)

Extract potential complementarities from other bins

Inputs:

bin_kos_per_module bins_alternatives module_to_map

microbetag.pathway_complementarity.a_modules_maps(kegg_modules_to_maps)

Get the KEGG maps in which a module takes part in

microbetag.pathway_complementarity.taxon_kos_per_module(bins_kos_df, ref_ko_per_module)

Keep track of the KOs related to a module present on each bin Input:

bins_kos_df (pd.DataFrame):

Return type:

bin_kos_per_module (Dict)

microbetag.pathway_complementarity.export_pathway_complementarities(config, bins_kos_df)

Function to get all the KEGG pathway complements among a set of bins

Input:

config (Config): instance of the microbetag Config class with settings bins_kos_df (pd.DataFrame): dictionary with bin id as a key and the KOs found in the bin as the value

Returns: {beneficiary_bin: {donor_bin_A: {module_a: [], module_b: [],.. }}}