Data analysis

Create table and graphical outputs:

source conf_cluster.conf
cd $OUT

module load autoload python/3.6.4
source $wd/env/bin/activate

sed -i 's/ /_/g' join_gene_id_seed.tab.pivot

Create a taxonomy Krona graph of all the community:

cd $OUT

t=6
for i in $SAMPLE_LIST; do
        ktImportTaxonomy -o $i.all.taxonomy.krona.html -t 1 -m $t join_gene_id_seed.tab.pivot
        t=$((t + 1))
done

Create a SEDD Krona graph of all the community:

s=6
for i in $SAMPLE_LIST; do
        paste <(cut -f$s join_gene_id_seed.tab.pivot) <(cut -f2,3,4,5 join_gene_id_seed.tab.pivot) > $i.all.seed.tab
        ktImportText $i.all.seed.tab -o $i.all.seed.html
        s=$((s + 1))
done

Create sub-table based on a SEED category:

python $wd/mining.py join_gene_id_seed.tab.pivot lev2 "Resistance_to_antibiotics_and_toxic_compounds"

Create taxonomy Krona graphs based on the sub-table:

m=6
for i in $SAMPLE_LIST; do

        ktImportTaxonomy -o $i.Resistance_to_antibiotics_and_toxic_compounds.taxonomy.krona.html -t 1 -m $m Resistance_to_antibiotics_and_toxic_compounds.seed_tax.tab
        m=$((m + 1))

done