#!/bin/bash
#SBATCH -t 4:00:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --mem=24g
#SBATCH --export=NONE
#SBATCH --mail-user=mramsey@uri.edu
#SBATCH --mail-type=BEGIN,END,FAIL

module load QIIME2/2019.7

rawdir=/data/mramseylab/raw_reads/2018_Serum/Merge_runs/
procdir=/data/mramseylab/proc_reads/
metadir=/data/mramseylab/metadata/
visdir=/data/mramseylab/visualizations/
cmr2="core-metrics-results-latest"
cmr="core-metrics-results"
# filter status of input files, "initial" is the 1st pass no filter at all
fil=-initial

#note change name of input tables for the 1st command below. Some input tables did not have standardized filename conventions
#changed to AF-hum-table.qza and table3.qza to minF-hum-table.qza
array=( minF AF SF NP )

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

qiime diversity alpha \
  --i-table  $procdir$i\-hum/$i\-hum-table.qza \
  --p-metric simpson_e \
  --output-dir $procdir$i\-hum/$cmr2

qiime diversity alpha-group-significance \
  --i-alpha-diversity $procdir$i\-hum/$cmr/shannon_vector.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $procdir$i\-hum/$cmr2/shannon_vector.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity $procdir$i\-hum/$cmr2/alpha_diversity.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $procdir$i\-hum/$cmr2/evenness-group-significance.qzv

done


#dual array taking the directories above and then running the next command on the 3 filenames in array2 for each directory prefix in array$
#note different array command syntax from above vs below
#array1=( minF AF SF NP )
#array2=( unweighted_unifrac_distance_matrix weighted_unifrac_distance_matrix bray_curtis_distance_matrix )

#for indirs in ${array1[@]}
#do
#    for infils in ${array2[@]}
#    do
#qiime diversity beta-group-significance \
#  --i-distance-matrix $procdir$indirs\-hum/$cmr/$infils\.qza \
#  --m-metadata-file  $metadir\Serum5.tsv \
#  --m-metadata-column Condition \
#  --o-visualization $procdir$indirs\-hum/$cmr/$infils\.qzv \
#  --p-pairwise

#    done
#done