Hack DRAM to calculate the coverage of all Kegg modules

Dram-get-all-modules.ipynb

I put everything in a neat script

If you have dram installed you have access to the mag_annotator module

annotation_file="path/to/annotation.tsv"
mouse_output_table= "all_kegg_modules.tsv"

import pandas as pd
from mag_annotator.utils import get_database_locs
from mag_annotator.summarize_genomes import build_module_net,make_module_coverage_frame

annotations = pd.read_csv(annotation_file, sep='\t', index_col=0)
db_locs = get_database_locs()
if 'module_step_form' not in db_locs:
    raise ValueError('Module step form location must be set in order to summarize genomes')

module_steps_form = pd.read_csv(db_locs['module_step_form'], sep='\t')

all_module_nets = {module: build_module_net(module_df)
                   for module, module_df in module_steps_form.groupby('module') }

module_coverage_frame = make_module_coverage_frame(annotations, all_module_nets, groupby_column='fasta')

module_coverage_frame.to_csv(mouse_output_table, sep='\t')