#!/bin/bash
#SBATCH -t 8:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=alex_labossiere@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

tablein=/data/mramseylab/raw_reads/AL_2022/denoise-table-1.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/plaque_meta_1.tsv
visdir=/data/mramseylab/visualizations/al_2022_1/
filtdir=/data/mramseylab/proc_reads/
# filter status of input files, "ctrl-filter" is just for taxa belonging to no template controls
fil=ctrl-filter-AL


#must make the directory you are filtering to 1st or else it will error
mkdir $filtdir$fil


qiime feature-table filter-samples \
  --i-table $tablein \
  --m-metadata-file $metadir \
  --p-where "[body-site]='control'" \
  --o-filtered-table $filtdir$fil/$fil-table-AL.qza

qiime taxa collapse \
  --i-table $filtdir$fil/$fil-table-AL.qza \
  --i-taxonomy $clsdir\silva-mod-taxonomy.qza \
  --p-level 6 \
  --o-collapsed-table $filtdir$fil/$fil-collapse-table-AL.qza

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

qiime tools export \
  --input-path $filtdir$fil/$fil-relative-collapse-table-AL.qza \
  --output-path $filtdir$fil/

biom convert \
-i $filtdir$fil/feature-table-.biom \
-o $filtdir$fil/$fil-relative-collapse-table-AL.txt \
--header-key “taxonomy” \
--to-tsv
#Not sure where the .biom file comes from
#Use above taxa table to filter out based on taxa present in controls

qiime feature-table filter-features \
  --i-table $tablein \
  --m-metadata-file $filtdir$fil/$fil-collapse-table-AL.qza \
  --o-filtered-table $filtdir$fil/$fil-excluded-table-AL.qza \
  --p-exclude-ids

#Use excluded table to generate barplot for checking

qiime taxa barplot \
  --i-table $filtdir$fil/$fil-excluded-table-AL.qza \
  --i-taxonomy $clsdir\silva-mod-taxonomy.qza \
  --m-metadata-file $metadir
  --o-visualization $filtdir$fil/$fil-excluded-table-AL.qzv
 
#Is this all to make sure we can properly filter out just the control