10.abundance_stats

source activate py3
set -eu

mkdir -p abundances
cd abundances
tsv_dir=./results
mkdir -p $tsv_dir

# parse the contig names out of the bin fasta files
python bin_contig_analysis.py -input ../metabat -output $tsv_dir/bin_contig_mappings.tsv

# calculate abundances.  Uses 20+ GB memory.  Could redsign script to iterate and append...
python aggregate.py -contig_path $tsv_dir/bin_contig_mappings.tsv -depth_path ../metabat/depth.txt -sample_info_dir ../data/sample_info/
mv bin_abundances.tsv $tsv_dir/bin_abundances.tsv

python summarise_bin_abundance_stats_with_bin_info.py