#!/bin/bash
#SBATCH -t 4:00:00
#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

treein=/data/mramseylab/raw_reads/2023_SUPP_V1V2/rooted-tree-master-v1v2-paired.qza
procdir=/data/mramseylab/proc_reads/2023_Master/
metadir=/data/mramseylab/metadata/plaque_meta_6.tsv
filtdir=/data/mramseylab/raw_reads/2023_SUPP_V1V2/master-denoise-table-v1v2-paired.qza


subjects=( subjectA subjectAn subjectJ subjectS ) #creates a list of subjects to use

for subject in "${subjects[@]}" #for variable (subject) in list, $ (open) list (subjects) use all in list ([@])
do

cmr="core-metric-results-$subject"
tabledir=/data/mramseylab/proc_reads/2023_Master/FilteredSamples/filter_feat_2_feq_5_$subject.qza

qiime diversity core-metrics-phylogenetic \
--i-phylogeny $treein \
--i-table $tabledir \
--p-sampling-depth 9000 \
--m-metadata-file $metadir \
--output-dir $procdir$cmr

qiime diversity alpha-group-significance \
--i-alpha-diversity $procdir$cmr/faith_pd_vector_fil_$subject.qza \
--m-metadata-file $metadir \
--o-visualization $procdir$cmr/faith-pd-group-significance_$subject.qzv

qiime diversity alpha-group-significance \
--i-alpha-diversity $procdir$cmr/evenness_vector_fil_$subject.qza \
--m-metadata-file $metadir \
--o-visualization $procdir$cmr/evenness-group-significance_$subject.qzv

array=( unweighted_unifrac_distance_matrix weighted_unifrac_distance_matrix bray_curtis_distance_matrix )

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

qiime diversity beta-group-significance \
--i-distance-matrix $procdir$cmr/"$i".qza \
--m-metadata-file $metadir \
--m-metadata-column media \
--o-visualization $procdir$cmr/"$i".qzv \
--p-pairwise

done
done