#!/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
echo "emails sent"
module load QIIME2/2024.2
echo "module loaded"

rawdir=/data/mramseylab/raw_reads/2023_AL_SUPP/triplicates/tripS/paired-pseudo-reps-seq-S.qza
clsdir=/data/mramseylab/16S/classifiers/homd-classifier
visdir=/data/mramseylab/16S/visualizations/AL_2024
procdir=/data/mramseylab/16S/visualizations/AL_2023/master-core-metrics-results-SubjectS-Saliva-only-6000
metadata=/data/mramseylab/16S/metadata/plaque_meta_S.tsv

#need to realign the representative sequences (yours) with classifer for taxonomic assignment

if
qiime feature-classifier classify-sklearn \
  --i-classifier $clsdir/HOMD-classifier.qza \
  --i-reads $rawdir \
  --o-classification $clsdir/subject-S-taxonomy-HOMD.qza; then 
	echo "taxonomy aligned"
fi


if
qiime metadata tabulate \
  --m-input-file $clsdir/subject-S-taxonomy-HOMD.qza \
  --o-visualization $clsdir/subject-S-taxonomy-HOMD.qzv; then
	echo "metadata table made"
fi
#qzv can be used to see classification and sequence asignemnt for blast if wanted

if qiime taxa barplot \
  --i-table $procdir/rarefied_table.qza \
  --i-taxonomy $clsdir/subject-S-taxonomy-HOMD.qza \
  --m-metadata-file $metadata \
  --o-visualization $visdir/taxabar-pseudo-S-trip.qzv; then
    echo "barplot made!"
fi
echo " Script DONE!!!!"