anvio_custom_hmm_coldshock.txt

# Database for all contigs already made, external-genomes.txt file already made

for i in *db
do
    anvi-run-hmms -c $i -H coldshock_hmm/
done

for i in *db
do
    # use basename for easier file naming
    base=$(basename $i .db)
    
    anvi-get-sequences-for-hmm-hits -c $i --hmm-source coldshock_hmm -o ${base}-sequences-for-hmm-hits.fa

done