#!/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/
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 core-metrics-phylogenetic \
  --i-phylogeny $rawdir\rooted-tree-merge.qza \
  --i-table  $procdir$i\-hum/$i\-hum-table.qza \
  --p-sampling-depth 5000 \
  --m-metadata-file $metadir\Serum5.tsv \
  --output-dir $procdir$i\-hum/$cmr

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

qiime diversity alpha-group-significance \
  --i-alpha-diversity $procdir$i\-hum/$cmr/evenness_vector.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $procdir$i\-hum/$cmr/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 1
#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