q2x_alphaDiversity.batch

#!/bin/bash
####  alpha diversity
#######################################################################################
set -euxo pipefail
cd $(dirname `readlink -f $0`)

prefix=`cat configuration.txt | grep "^prefix" | cut -d "=" -f 2`
manifest="${prefix}_manifest"
prefix_dada2="${prefix}_da2"
prefix_unoise3="${prefix}_un3"
prefix_uparse="${prefix}_up"
work_dir="alphaDiversity"

dada2_tab="${prefix_dada2}_tab_pk_filtered_rarefy"
unoise3_tab="${prefix_unoise3}_tab_pk_filtered_rarefy"
uparse_tab="${prefix_uparse}_tab_pk_filtered_rarefy"

unoise3_tree_tab="${prefix_unoise3}_tab_pk_ftre2flt_filtered_rarefy"
dada2_tree_tab="${prefix_dada2}_tab_pk_ftre2flt_filtered_rarefy"
uparse_tree_tab="${prefix_uparse}_tab_pk_ftre2flt_filtered_rarefy"


dada2_tree="${prefix_dada2}_rep_pk_ftre.qza"
unoise3_tree="${prefix_unoise3}_rep_pk_ftre.qza"
uparse_tree="${prefix_uparse}_rep_pk_ftre.qza"


echo "#============ This script is going to output these files ..."
echo
echo "alphaDiversity/ (a directory containing the alpha-diversity results)"
echo
echo "#============ running batch ..."

if [ ! -d ${work_dir} ];then
	mkdir ${work_dir}
else
	rm -rf ${work_dir}
	mkdir ${work_dir}
fi

alphaAnalysis(){
	
	qiime diversity alpha-group-significance \
	--i-alpha-diversity ${work_dir}/${prefix_tab}_${metric}_vector.qza \
	--m-metadata-file ${prefix}_manifest.tsv \
	--o-visualization ${work_dir}/${prefix_tab}_${metric}_significance.qzv
	
	qiime metadata tabulate \
	--m-input-file ${work_dir}/${prefix_tab}_${metric}_vector.qza \
	--o-visualization ${work_dir}/${prefix_tab}_${metric}_tab.qzv
}
	
#α diversity
for metric in shannon simpson chao1 ace pielou_e goods_coverage observed_features
do
	for tab in  ${unoise3_tab} ${dada2_tab} ${uparse_tab}
	do
		prefix_tab=${tab%_tab*}
		qiime diversity alpha \
		--i-table ${tab}.qza \
		--p-metric ${metric} \
		--o-alpha-diversity ${work_dir}/${prefix_tab}_${metric}_vector.qza
		
		alphaAnalysis
	done
done


#α diversity(phylogenetic)
for tab in ${unoise3_tree_tab} ${dada2_tree_tab} ${uparse_tree_tab}
do
	prefix_tab=${tab%_tab*}
	tree=${prefix_tab}_rep_pk_ftre
	metric="faith_pd"
	qiime diversity alpha-phylogenetic \
	--i-table ${tab}.qza \
	--i-phylogeny ${tree}.qza \
	--p-metric ${metric} \
	--o-alpha-diversity ${work_dir}/${prefix_tab}_${metric}_vector.qza
	alphaAnalysis
done

#Merging the alphaDiversity vectors in a table.
for tab in ${prefix_unoise3} ${prefix_dada2} ${prefix_uparse}
do
	merge_command="qiime metadata tabulate"
	for metric in shannon simpson chao1 ace pielou_e goods_coverage observed_features faith_pd
	do
		merge_command="${merge_command} --m-input-file ${work_dir}/${tab}_${metric}_vector.qza"
	done    
	${merge_command} --o-visualization ${work_dir}/${tab}_alphaDiversity_tab.qzv
done    

exit 0