Convert metaphlan marker_counts output to raw count matrix

1. Analyse your samples with metaphlan:

The marker_counts parameter is required to output the count per marker gene:

metaphlan --input_type fastq --bowtie2db metaphlan_db -t marker_counts -o sample_count.tsv metagenome_1.fastq,metagenome_2.fastq

2. Aggregate your counts at SGB level

The aggregation at SGB level can be performed with the following command:

python3 aggregate_SBG.py sample_count.tsv mpa_vOct22_CHOCOPhlAnSGB_202212_SGB_len.txt.gz sample_name sample_aggregated.tsv

The counts are normalized according to the length of the marker gene to a default length of 1000.

3. Build the count matrix and the taxonomy matrix

For each sample, we can aggregate them with the following command:

python3 build_matrix.py sample1_aggregated.tsv sample2_aggregated.tsv ... output_counts.tsv output_taxonomy.tsv