#!/bin/bash
cd /home/qiime2/qiime2-moving-pictures-tutorial/
export PATH=/miniconda3/bin:$PATH
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
source tab-qiime

qiime tools import \
  --type EMPSingleEndSequences \
  --input-path emp-single-end-sequences \
  --output-path emp-single-end-sequences.qza



qiime demux emp-single \
  --i-seqs emp-single-end-sequences.qza \
  --m-barcodes-file sample-metadata.tsv \
  --m-barcodes-category BarcodeSequence \
  --o-per-sample-sequences demux.qza


qiime demux summarize \
  --i-data demux.qza \
  --o-visualization demux.qzv


qiime dada2 plot-qualities \
  --i-demultiplexed-seqs demux.qza \
  --p-n 10 \
  --o-visualization demux-qual-plots.qzv

qiime dada2 denoise-single \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left 0 \
  --p-trunc-len 100 \
  --o-representative-sequences rep-seqs.qza \
  --o-table table.qza


qiime feature-table summarize \
  --i-table table.qza \
  --o-visualization table.qzv \
  --m-sample-metadata-file sample-metadata.tsv


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


qiime alignment mafft \
  --i-sequences rep-seqs.qza \
  --o-alignment aligned-rep-seqs.qza


qiime alignment mask \
  --i-alignment aligned-rep-seqs.qza \
  --o-masked-alignment masked-aligned-rep-seqs.qza


qiime phylogeny fasttree \
  --i-alignment masked-aligned-rep-seqs.qza \
  --o-tree unrooted-tree.qza

qiime phylogeny midpoint-root \
  --i-tree unrooted-tree.qza \
  --o-rooted-tree rooted-tree.qza

qiime diversity core-metrics \
  --i-phylogeny rooted-tree.qza \
  --i-table table.qza \
  --p-sampling-depth 1441 \
  --output-dir cm1441



qiime diversity alpha-group-significance \
  --i-alpha-diversity cm1441/faith_pd_vector.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization cm1441/faith-pd-group-significance.qzv

qiime diversity alpha-group-significance \
  --i-alpha-diversity cm1441/evenness_vector.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization cm1441/evenness-group-significance.qzv



qiime diversity alpha-correlation \
  --i-alpha-diversity cm1441/faith_pd_vector.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization cm1441/faith-pd-correlation.qzv



qiime diversity alpha-correlation \
  --i-alpha-diversity cm1441/evenness_vector.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization cm1441/evenness-correlation.qzv


qiime diversity beta-group-significance \
  --i-distance-matrix cm1441/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-category BodySite \
  --o-visualization cm1441/unweighted-unifrac-body-site-significance.qzv

qiime diversity beta-group-significance \
  --i-distance-matrix cm1441/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-category Subject \
  --o-visualization cm1441/unweighted-unifrac-subject-group-significance.qzv



qiime diversity bioenv \
  --i-distance-matrix cm1441/unweighted_unifrac_distance_matrix.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization cm1441/unweighted-unifrac-bioenv.qzv

qiime diversity bioenv \
  --i-distance-matrix cm1441/bray_curtis_distance_matrix.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization cm1441/bray-curtis-bioenv.qzv


qiime emperor plot \
  --i-pcoa cm1441/unweighted_unifrac_pcoa_results.qza \
  --m-metadata-file sample-metadata.tsv \
  --p-custom-axis DaysSinceExperimentStart \
  --o-visualization cm1441/unweighted-unifrac-emperor.qzv

qiime emperor plot \
  --i-pcoa cm1441/bray_curtis_pcoa_results.qza \
  --m-metadata-file sample-metadata.tsv \
  --p-custom-axis DaysSinceExperimentStart \
  --o-visualization cm1441/bray-curtis-emperor.qzv

qiime feature-classifier classify \
  --i-classifier gg-13-8-99-515-806-nb-classifier.qza \
  --i-reads rep-seqs.qza \
  --o-classification taxonomy.qza

qiime taxa tabulate \
  --i-data taxonomy.qza \
  --o-visualization taxonomy.qzv

qiime taxa barplot \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization taxa-bar-plots.qzv

qiime composition add-pseudocount \
  --i-table table.qza \
  --o-composition-table comp-table.qza

qiime composition ancom \
  --i-table comp-table.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-category BodySite \
  --o-visualization ancom-BodySite.qzv


qiime taxa collapse \
  --i-table table.qza \
  --i-taxonomy taxonomy.qza \
  --p-level 2 \
  --o-collapsed-table table-l2.qza

qiime composition add-pseudocount \
  --i-table table-l2.qza \
  --o-composition-table comp-table-l2.qza

qiime composition ancom \
  --i-table comp-table-l2.qza \
  --m-metadata-file sample-metadata.tsv \
  --m-metadata-category BodySite \
  --o-visualization l2-ancom-BodySite.qzv