oggmap.eggnog2orthomap module

Author: Kristian K Ullrich date: February 2025 email: ullrich@evolbio.mpg.de License: GPL-3

oggmap.eggnog2orthomap.add_argparse_args(parser: ArgumentParser)

This function attaches individual argument specifications to the parser.

Parameters:

parser (argparse.ArgumentParser) – An argparse.ArgumentParser.

oggmap.eggnog2orthomap.define_parser()

A helper function for using eggnog2orthomap.py via the terminal.

Returns:

An argparse.ArgumentParser.

Return type:

argparse.ArgumentParser

oggmap.eggnog2orthomap.get_eggnog_orthomap(qt, og, subset=None, out=None, quiet=False, continuity=True, overwrite=True, ncbi=None, dbname=None)

This function return an orthomap for a given query species and eggnog input data.

Parameters:

  • qt (str) – Query species taxID.

  • og (str) – Path to eggnog <e6.og2seqs_and_species.tsv> file.

  • subset (str) – Path to file containing orthologous groups to include.

  • out (str) – Path to output file.

  • quiet (bool) – Specify if output should be quiet.

  • continuity (bool) – Specify if continuity score should be calculated.

  • overwrite (bool) – Specify if output should be overwritten.

  • ncbi (dict) – The NCBI taxonomic database.

  • dbname (str) – Specify taxadb.sqlite file.

Returns:

A list of results such as: orthomap, species_list, youngest_common_counts

Return type:

list

Example

>>>
oggmap.eggnog2orthomap.main()

The main function that is being called when eggnog2orthomap is used via the terminal.