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run_ancom.sh
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#!/bin/bash
file=$1
dir=$2
metadata=$3
column=$4
taxonomy=$5
#ANCOM
prefix=${i_table%.qza}
qiime composition add-pseudocount --i-table "$i_table" --output-dir "$dir"/ancom --o-composition-table "$dir"/ancom/"$prefix"_comp.qza
qiime composition ancom --i-table "$dir"/ancom/"$prefix"_comp.qza --m-metadata-file "$metadata" --m-metadata-column "$column" --o-visualization "$dir"/ancom/"$prefix"-ancom-"$column".qzv
qiime taxa collapse --i-table "$i_table" --i-taxonomy "$taxonomy" --p-level 2 --o-collapsed-table "$dir"/ancom/"$prefix"-l2.qza
qiime composition add-pseudocount --i-table "$dir"/ancom/"$prefix"-l2.qza --o-composition-table "$dir"/ancom/"$prefix"-comp-l2.qza
qiime composition ancom --i-table "$dir"/ancom/"$prefix"-comp-l2.qza --m-metadata-file "$metadata" --m-metadata-column "$column" --o-visualization "$dir"/ancom/"$prefix"-level_2-ancom-"$column".qzv
qiime taxa collapse --i-table "$i_table" --i-taxonomy "$taxonomy" --p-level 5 --o-collapsed-table "$dir"/ancom/"$prefix"-l5.qza
qiime composition add-pseudocount --i-table "$dir"/ancom/"$prefix"-l5.qza --o-composition-table "$dir"/ancom/"$prefix"-comp-l5.qza
qiime composition ancom --i-table "$dir"/ancom/"$prefix"-comp-l5.qza --m-metadata-file "$metadata" --m-metadata-column "$column" --o-visualization "$dir"/ancom/"$prefix"-level_5-ancom-"$column".qzv
qiime taxa collapse --i-table "$i_table" --i-taxonomy "$taxonomy" --p-level 6 --o-collapsed-table "$dir"/ancom/"$prefix"-l6.qza
qiime composition add-pseudocount --i-table "$dir"/ancom/"$prefix"-l6.qza --o-composition-table "$dir"/ancom/"$prefix"-comp-l6.qza
qiime composition ancom --i-table "$dir"/ancom/"$prefix"-comp-l6.qza --m-metadata-file "$metadata" --m-metadata-column "$column" --o-visualization "$dir"/ancom/"$prefix"-level_6-ancom-"$column".qzv