#!/bin/bash
#SBATCH -t 6:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/
visdir=/data/mramseylab/visualizations/
filtdir=/data/mramseylab/proc_reads/
rawdir=/data/mramseylab/raw_reads/2018_Serum/Merge_runs/
procdir=/data/mramseylab/proc_reads/

array=( minF-hum AF-hum SF-hum NP-hum )

for i in "${array[@]}"
do

qiime taxa collapse \
 --i-table $filtdir$i/$i\-table.qza \
 --i-taxonomy $clsdir\silva-mod-taxonomy2.qza \
 --p-level 7 \
 --o-collapsed-table $filtdir$i/$i\-table.collapse.qza \

qiime feature-table relative-frequency \
 --i-table $filtdir$i/$i\-table.collapse.qza \
 --o-relative-frequency-table $filtdir$i/$i\-table.rel-collapse.qza

qiime tools export \
 --input-path $filtdir$i/$i\-table.rel-collapse.qza \
 --output-path $filtdir$i/

#note, must use single hashes for -i / -o unlike other qiime commands. 
biom convert \
 -i $filtdir$i/feature-table.biom \
 -o $filtdir$i/$i\-table.txt \
 --header-key “taxonomy” \
 --to-tsv

done