#!/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 composition add-pseudocount \
  --i-table $filtdir$i/$i\-table.qza \
  --o-composition-table $filtdir$i/comp-$i\-table.qza

#"Condition" is from the metadata and is for Healthy, T2D, T2DP categories
qiime composition ancom \
  --i-table $filtdir$i/comp-$i\-table.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --m-metadata-column Condition \
  --o-visualization $filtdir$i/$i\-ancom-Condition.qzv

#test at the taxonomic species level (#7)
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\-7-table.qza

qiime composition add-pseudocount \
  --i-table $filtdir$i/$i\-7-table.qza \
  --o-composition-table $filtdir$i/comp-$i\-7-table.qza

qiime composition ancom \
  --i-table $filtdir$i/comp-$i\-7-table.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --m-metadata-column Condition \
  --o-visualization $filtdir$i/Condition-$i\-7-table.qzv

#Condition for level 3
qiime taxa collapse \
  --i-table $filtdir$i/$i\-table.qza \
  --i-taxonomy $clsdir\silva-mod-taxonomy2.qza \
  --p-level 3 \
  --o-collapsed-table $filtdir$i/$i\-3-table.qza

qiime composition add-pseudocount \
  --i-table $filtdir$i/$i\-3-table.qza \
  --o-composition-table $filtdir$i/comp-$i\-3-table.qza

qiime composition ancom \
  --i-table $filtdir$i/comp-$i\-3-table.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --m-metadata-column Condition \
  --o-visualization $filtdir$i/comp-$i\-3-table.qzv

#Ancom for entire T2.status
qiime composition ancom \
  --i-table $filtdir$i/comp-$i\-table.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --m-metadata-column T2.status \
  --o-visualization $filtdir$i/$i\-ancom-T2.status.qzv

  #test at the taxonomic species level (#7)
  qiime composition ancom \
    --i-table $filtdir$i/comp-$i\-7-table.qza \
    --m-metadata-file $metadir\Serum5.tsv \
    --m-metadata-column T2.status \
    --o-visualization $filtdir$i/T2.status-$i\-7-table.qzv

#test at the taxonomic species level (#3)
qiime composition ancom \
  --i-table $filtdir$i/comp-$i\-3-table.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --m-metadata-column T2.status \
  --o-visualization $filtdir$i/T2.status-$i\-3-table.qzv

done