gistfile1.txt

ls summary-proteins-* | \
proteins-to-pathogens.py \
    --format fastq \
    --html \
    --minProteinFraction 0.1 \
    --pathogenType bacterial \
    --proteinFastaFilename $HOME/rdsbt/root/share/ncbi/bacterial-refseq/20180609-bacteria.nonredundant_protein.fasta.gz \
    --pathogenPanelFilename bacteria.png \
    --sampleIndexFilename samples.index \
    --pathogenIndexFilename pathogens.index \
    > index.html