#!/bin/bash

#Move to data directory from starting directory
cd..

cd data

#Make team project working directory
mkdir project2

#Import demultiplexed sequences in metadata
qiime tools import \
--type 'SampleData[SequencesWithQuality]' \
--input-path /mnt/datasets/project_2/dog/dog_manifest.txt \
--output-path demux.qza \
--input-format SingleEndFastqManifestPhred33V2

#Generate a visualization of the demultiplexing results
qiime demux summarize \
--i-data demux.qza \
--o-visualization demux.qzv

#Use DADA2 sequence quality control to determine ASVs after trimming the sequences at appropriate locations
qiime dada2 denoise-single \
--i-demultiplexed-seqs demux.qza \
--p-trim-left 0 \
--p-trunc-len 84 \
--o-representative-sequences rep-seqs-dada2.qza \
--o-table table-dada2.qza \
--o-denoising-stats stats-dada2.qza

#Visualize DADA2 stats
qiime metadata tabulate \
--m-input-file stats-dada2.qza \
--o-visualization stats-dada2.qzv

#Visualize ASV stats
qiime feature-table summarize \
--i-table table-dada2.qza \
--o-visualization table-dada2.qzv \
--m-sample-metadata-file /mnt/datasets/project_2/dog/dog_metadata.txt

qiime feature-table tabulate seqs \
--i-data rep-seqs-dada2.qza \
--o-visualization rep-seqs.qzv

#Filter metadata to include only samples of dogs with IBD in a filtered feature table
qiime feature-table filter-samples \
--i-table table-dada2.qza \
--m-metadata-file /mnt/datasets/project_2/dog/dog_metadata.txt \
--p-where "[disease_stat]='IBD'" \
--o-filtered-table IBD-only-filtered-table.qza

#Generate a tree for phylogenetic diversity analyses 
qiime phylogeny align-to-tree-mafft-fasttree \
--i-sequences rep-seqs-dada2.qza \
--o-alignment aligned-rep-seqs.qza \
--o-masked-alignment masked-aligned-rep-seqs.qza \
--o-tree unrooted-tree.qza \
--o-rooted-tree rooted-tree.qza

#Generate rarefaction visualization
qiime diversity alpha-rarefaction \
--i-table IBD-only-filtered-table.qza \
--i-phylogeny rooted-tree.qza \
--p-max-depth 28653 \
--m-metadata-file /mnt/datasets/project_2/dog/dog_metadata.txt \
--o-visualization alpha-rarefaction.qzv