microbetag.helpers

Handlers classes allowing the different steps

Module Contents

class microbetag.helpers.PathwayComplementarity(config)

Sets variables regarding pathway complementarity tasks based on user’s config (.yml) file

setup_kegg_annotations()

Sets up KEGG annotations and directories.

get_kofam_db_path()

Returns the KOfam database path.

handle_missing_kofam_db()

Handles the case when the KOfam database path is missing.

initialize(conf)

Main function to initialize pathway complementarity settings.

setup_ko_merged()

Sets up the KO merged file.

output_dirs(config)

Paths to output folders and files

class microbetag.helpers.MappingPaths(config)

Sets paths to mapping files

class microbetag.helpers.Faprotax(config)

class microbetag.helpers.NetworkHandler(config)

process_network(config)

Process network edgelist and check bin consistency.

class microbetag.helpers.AbdTableHandler(config)

load_abundance_table(config)

Reads and validates the abundance table.

load_metadata_file(config)

Load metadata file if provided

class microbetag.helpers.BinsHandler(config)

class microbetag.helpers.SeedComplementarityHandler(config)

seeds_paths(config)

Set pathways for seeds related files and folders

microbetag.helpers.manta_input_net(config)

Build intermediate network file as input for manta

class microbetag.helpers.Emojis

microbetag.helpers.local_seed_url()

Builds KEGG urls for seed complements. Function to be used out of the pipeline