microbetag.config

Module Contents

microbetag.config.load_abundance(abd_file)

Load a tsv/csv format abundance table assuming the sequence id is procided in the first column and the taxonomy in the last one

Return seq_id_to_taxonomy:

A pd.DataFrame with the sequence id and their corresponding genome

Return sequence_id_column_name:

The name (str) of the column with the sequence identifier (e.g. seqId)

Return taxonomy_column_name:

The name (str) of the column with the taxonomy

class microbetag.config.Config(conf, config_file)

Parses a microbetag configuration file (yaml) to init a microbetag run.

export_to_log(log_file='parameters.log')