#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=288g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2024.2

clsdir=/data/mramseylab
filtdir=/data/mramseylab
rawdir=/data/mramseylab/
procdir=/data/mramseylab/

tabledir=/data/mramseylab/16S/proc_reads/2024_AL_SUPP_6000/FST0
clsdir=/data/mramseylab/16S/classifiers/homd-classifier/taxonomy.qza
visdir=/data/mramseylab/16S/visualizations/AL_2024/FST0-filtered
metadir=/data/mramseylab/16S/metadata/meta_BSFS.tsv


qiime taxa collapse \
 --i-table $tabledir/filtered-reads.qza \
 --i-taxonomy $clsdir \
 --p-level 6 \
 --o-collapsed-table $tabledir/taxa-collpased-lvl-6.qza \

qiime feature-table relative-frequency \
 --i-table $tabledir/taxa-collpased-lvl-6.qza \
 --o-relative-frequency-table $tabledir/rel-feq-feat-table-lefse.qza

qiime tools export \
 --input-path $tabledir/rel-feq-feat-table-lefse.qza \
 --output-path $tabledir/

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

done