#!/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

#note new $tablein below as we are now working on human only samples filtered in meta-filter.sh
tablein=/data/mramseylab/proc_reads/initial-human/initial-human-table.qza
clsdir=/data/mramseylab/classifiers/
metadir=/data/mramseylab/metadata/
visdir=/data/mramseylab/visualizations/

# filter status of input files, "minF-hum" is minimal filtered human only data
fil=minF-hum
filtdir=/data/mramseylab/proc_reads/$fil/

#must make the directory you are filtering to 1st or else it will error
mkdir $filtdir

#filter features that appear less than 10 times across all samples
qiime feature-table filter-features \
  --i-table $tablein \
  --p-min-frequency 10 \
  --o-filtered-table $filtdir\table1.qza

#Making visualization at each step to monitor loss of taxa numbers
qiime feature-table summarize \
  --i-table $filtdir\table1.qza \
  --o-visualization $filtdir\table1.qzv \
  --m-sample-metadata-file $metadir\Serum5.tsv

#filter for features present in more than 2 libraries (used 2 instead of 1 due to combined runs)
qiime feature-table filter-features \
  --i-table $filtdir\table1.qza \
  --p-min-samples 3 \
  --o-filtered-table $filtdir\table2.qza

qiime feature-table summarize \
  --i-table $filtdir\table2.qza \
  --o-visualization $filtdir\table2.qzv \
  --m-sample-metadata-file $metadir\Serum5.tsv

#Filter things with less than 20 reads per sample
qiime feature-table filter-samples \
  --i-table $filtdir\table2.qza \
  --p-min-frequency 20 \
  --o-filtered-table $filtdir\table3.qza

qiime feature-table summarize \
  --i-table $filtdir\table3.qza \
  --o-visualization $filtdir\table3.qzv \
  --m-sample-metadata-file $metadir\Serum5.tsv

#View the *qzv tables and determine the sampling depth for the next steps (align-to-tree-mafft-fasttree)

#Use excluded table to generate barplot for checking

cp $filtdir\table3.qza $filtdir$fil-excluded-table.qza

qiime taxa barplot \
  --i-table $filtdir$fil-excluded-table.qza \
  --i-taxonomy $clsdir\silva-mod-taxonomy2.qza \
  --m-metadata-file $metadir\Serum5.tsv \
  --o-visualization $filtdir$fil-excluded-table.qzv

#Generate viewable feature table to look for ASVs of interest / filtering stats
qiime feature-table summarize \
  --i-table $filtdir$fil-excluded-table.qza \
  --o-visualization $filtdir$fil-excluded-table2.qzv \
  --m-sample-metadata-file $metadir\Serum5.tsv