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q2pipe_step11_export.sh
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q2pipe_step11_export.sh
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#!/bin/bash
################################
# #
# Qiime 2 Pipeline #
# By: Patrick Gagne (NRCan) #
# Step 11 - Exportation #
# December 16, 2022 #
# #
################################
exit_on_error(){
echo "Qiime2 command error detected"
echo "Exiting program"
exit 1
}
optionfile=$1
if [ ! $optionfile ] || [ ! -e $optionfile ] || [ ! -r $optionfile ]
then
echo "ERROR: you must specify a valid, accessible qiime2 optionfile"
exit 1
fi
source $optionfile
if [ $TEMPORARY_DIRECTORY ]
then
echo "Overriding default temporary directory to $TEMPORARY_DIRECTORY"
if [ ! -d $TEMPORARY_DIRECTORY ] || [ ! -w $TEMPORARY_DIRECTORY ]
then
echo "ERROR: $TEMPORARY_DIRECTORY does not exist or is read only"
exit 2
fi
export TMPDIR=$TEMPORARY_DIRECTORY
fi
if [ ! $TMPDIR ]
then
export TMPDIR=/tmp
fi
if [ "$APPTAINER_COMMAND" != "" ]
then
echo "DEBUG: Checking temporary folder"
temp_check=$( $APPTAINER_COMMAND mktemp -t Q2PIPE_TEMPFOLDER_CHECK.XXXXXX.temp )
bname=$( basename $temp_check )
if [ ! -e $TMPDIR/$bname ]
then
echo "ERROR: Disparity between Apptainer temporary folder and system temporary folder"
echo "Please make sure both are pointing to the same folder"
exit 5
else
echo "DEBUG: Temporary file check status: OK"
rm $TMPDIR/Q2PIPE_TEMPFOLDER_CHECK.??????.temp
fi
fi
if [ "$GENERATE_ANCOM" == "true" ] && [ ! $m_metadata_column ]
then
echo "ERROR: m_metadata_column not set in the option file"
echo "This parameter is mandatory for ANCOM analysis"
exit 3
fi
if [ "$SKIP_RAREFACTION" == "true" ] || [ "$SKIP_RAREFACTION" == "both" ]
then
$APPTAINER_COMMAND qiime tools export \
--input-path $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
--output-path $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity"
$APPTAINER_COMMAND biom convert \
-i $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity"/feature-table.biom \
-o $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity"/$ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".tsv --to-tsv
$APPTAINER_COMMAND qiime tools export \
--input-path $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
--output-path $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"
sed -i 's/Feature ID/#OTUID/g' $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/taxonomy.tsv
sed -i 's/Taxon/taxonomy/g' $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/taxonomy.tsv
sed -i 's/Confidence/confidence/g' $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/taxonomy.tsv
$APPTAINER_COMMAND biom add-metadata \
-i $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity"/feature-table.biom \
--observation-metadata-fp $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/taxonomy.tsv \
--sc-separated taxonomy \
-o $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/feature_taxonomy_merged.biom
$APPTAINER_COMMAND biom convert \
-i $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/feature_taxonomy_merged.biom \
-o $ANALYSIS_NAME.ASV_table_norarefaction_dn"$p_perc_identity".tsv --to-tsv --header-key taxonomy
sed -i '1d' $ANALYSIS_NAME.ASV_table_norarefaction_dn"$p_perc_identity".tsv
$APPTAINER_COMMAND qiime tools export \
--input-path $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza \
--output-path $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"
if [ "$( $APPTAINER_COMMAND which ASV_Table_DNA_Merger.py )" != "" ]
then
$APPTAINER_COMMAND ASV_Table_DNA_Merger.py \
--fasta $ANALYSIS_NAME.asv_tax_dir_dn"$p_perc_identity"/dna-sequences.fasta \
--asv-table $ANALYSIS_NAME.ASV_table_norarefaction_dn"$p_perc_identity".tsv \
--out $ANALYSIS_NAME.ASV_tableSeqs_norarefaction_dn"$p_perc_identity".tsv || echo "WARNING: ASV_Table_DNA_Merger not installed"
else
echo "WARNING: ASV_Table_DNA_Merger.py not available in PATH"
echo "ASV table merge with DNA sequences cannot be done"
fi
if [ "$GENERATE_FUNGUILD" == "true" ]
then
echo "Running FUNGuild analysis..."
$APPTAINER_COMMAND Guilds_v1.1.py \
-otu $ANALYSIS_NAME.ASV_table_norarefaction_dn"$p_perc_identity".tsv \
-m -u -db $FUNGUILD_DATABASE_PATH
fi
fi
if [ "$SKIP_RAREFACTION" == "false" ] || [ "$SKIP_RAREFACTION" == "both" ]
then
$APPTAINER_COMMAND qiime tools export \
--input-path $ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity".qza \
--output-path $ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity"
$APPTAINER_COMMAND biom convert \
-i $ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity"/feature-table.biom \
-o $ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity"/$ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity".tsv --to-tsv
$APPTAINER_COMMAND qiime tools export \
--input-path $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
--output-path $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"
sed -i 's/Feature ID/#OTUID/g' $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/taxonomy.tsv
sed -i 's/Taxon/taxonomy/g' $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/taxonomy.tsv
sed -i 's/Confidence/confidence/g' $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/taxonomy.tsv
$APPTAINER_COMMAND biom add-metadata \
-i $ANALYSIS_NAME.rarefied_"$p_sampling_depth"_filtered_table_dn"$p_perc_identity"/feature-table.biom \
--observation-metadata-fp $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/taxonomy.tsv \
--sc-separated taxonomy \
-o $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/feature_taxonomy_merged.biom
$APPTAINER_COMMAND biom convert \
-i $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/feature_taxonomy_merged.biom \
-o $ANALYSIS_NAME.ASV_table_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".tsv --to-tsv --header-key taxonomy
sed -i '1d' $ANALYSIS_NAME.ASV_table_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".tsv
$APPTAINER_COMMAND qiime tools export \
--input-path $ANALYSIS_NAME.filtered_rep-seqs-dada2_dn"$p_perc_identity".qza \
--output-path $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"
if [ "$( $APPTAINER_COMMAND which ASV_Table_DNA_Merger.py )" != "" ]
then
$APPTAINER_COMMAND ASV_Table_DNA_Merger.py \
--fasta $ANALYSIS_NAME.asv_tax_dir_rarefied_"$p_sampling_depth"_dn"$p_perc_identity"/dna-sequences.fasta \
--asv-table $ANALYSIS_NAME.ASV_table_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".tsv \
--out $ANALYSIS_NAME.ASV_tableSeqs_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".tsv || echo "WARNING: ASV_Table_DNA_Merger not installed"
else
echo "WARNING: ASV_Table_DNA_Merger.py not available in PATH"
echo "ASV table merge with DNA sequences cannot be done"
fi
if [ "$GENERATE_FUNGUILD" == "true" ]
then
echo "Running FUNGuild analysis..."
$APPTAINER_COMMAND Guilds_v1.1.py \
-otu $ANALYSIS_NAME.ASV_table_rarefied_"$p_sampling_depth"_dn"$p_perc_identity".tsv \
-m -u -db $FUNGUILD_DATABASE_PATH
fi
fi
if [ $EXTRACTION_FORM_PATH ]
then
if [ ! -e $EXTRACTION_FORM_PATH ]
then
echo "ERROR: Extraction form $EXTRACTION_FORM_PATH not found"
exit 1
fi
echo "Extracting results files according to $EXTRACTION_FORM_PATH"
mkdir "$ANALYSIS_NAME"_form_extraction 2>/dev/null
head -n 1 $EXTRACTION_FORM_PATH > "$ANALYSIS_NAME"_form_extraction/extraction_form.tsv
# NOTICE: use sed 's/,/ /g' to remove , from the file before converting to CSV (better to not use , in form)
cat $EXTRACTION_FORM_PATH | sed 's/\t/,/g' | while read line
do
if [ "$( echo $line | awk -F',' '{ print $2 }' )" != "True" ]
then
continue
fi
#echo $line
if [ "$( echo $line | grep MANIFEST_NAME )" != "" ]
then
filetype=$( echo $line | awk -F',' '{ print $6 }' | sed 's;./MANIFEST_NAME/MANIFEST_NAME.;;g' )
filenames=$( find -maxdepth 2 -mindepth 2 -wholename "./*/*.$filetype" -type f )
cp -R --parent $filenames "$ANALYSIS_NAME"_form_extraction/
echo $line | sed 's/,/\t/g' >> "$ANALYSIS_NAME"_form_extraction/extraction_form.tsv
continue
fi
not_found_tag=0
filename=$( echo $line | awk -F',' '{ print $6 }' | sed "s/ANALYSIS_NAME/$ANALYSIS_NAME/g" | sed "s/RARELEVEL/$p_sampling_depth/g" | sed "s/FREQLEVEL/$p_min_frequency/g" | sed "s/SAMPLEVEL/$p_min_samples/g" | sed "s/CLUSTID/$p_perc_identity/g" )
# Looping trough files is better for multiple folder cases (beta_metrics)
for files in $filename
do
#echo $files
if [ ! -e $files ]
then
not_found_tag=1
fi
done
if [ $not_found_tag -eq 1 ]
then
echo "WARNING: $filename not found"
continue
fi
#echo $filename
#if [ ! -e $filename ]
#then
# echo "WARNING: $filename not found"
# continue
#fi
cp -R --parent $filename "$ANALYSIS_NAME"_form_extraction/
echo $line | sed 's/,/\t/g' >> "$ANALYSIS_NAME"_form_extraction/extraction_form.tsv
done
fi
if [ "$GENERATE_ANCOM" == "true" ]
then
echo "Preparing ANCOM analysis"
if [ ! -d "$ANALYSIS_NAME"_ANCOM ]
then
mkdir "$ANALYSIS_NAME"_ANCOM
fi
$APPTAINER_COMMAND qiime taxa collapse \
--i-table $ANALYSIS_NAME.filtered_table_dn"$p_perc_identity".qza \
--i-taxonomy $ANALYSIS_NAME.taxo_dn"$p_perc_identity".qza \
--p-level $p_level \
--o-collapsed-table "$ANALYSIS_NAME"_ANCOM/feature_table_ANCOM.qza || exit_on_error
$APPTAINER_COMMAND qiime composition add-pseudocount \
--i-table "$ANALYSIS_NAME"_ANCOM/feature_table_ANCOM.qza \
--o-composition-table "$ANALYSIS_NAME"_ANCOM/composition_table_ANCOM.qza || exit_on_error
m_metadata_column=$( echo $m_metadata_column | sed 's/,/ /g' )
for col in $m_metadata_column
do
echo "Generating ANCOM for column $col"
$APPTAINER_COMMAND qiime composition ancom \
--i-table "$ANALYSIS_NAME"_ANCOM/composition_table_ANCOM.qza \
--m-metadata-file $METADATA_FILE_PATH \
--m-metadata-column $col \
--o-visualization "$ANALYSIS_NAME"_ANCOM/ANCOM_"$col"_results.qzv || exit_on_error
done
fi