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ETL_population_pipeline.sh
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ETL_population_pipeline.sh
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#!/usr/bin/env bash
help="
#####################################################
# #
# ITSoneDB upgrade program #
# ETL_population_pipeline #
# #
#####################################################
This script menages the procedure to populate etl directory after
ITSoneDB_upgrade_pipeline procedure completion.
USAGE:
$./ETL_population_pipeline.sh
-s directory of scripts menaged by this .sh
-n release number
-r releases directory
-p previous release number
"
if [[ $# -eq 0 ]] # se lo script è eseguito senza argomenti...
then
echo -e "$help" # ... stampo l'help...
exit 1 # ... ed esco.
fi
while getopts ":h:s:n:r:p:" opzione
do
case "${opzione}" in
s) scripts=${OPTARG};;
#x) aux=${OPTARG};;
n) release=${OPTARG};;
r) releases=${OPTARG};;
p) prevrel=${OPTARG};;
h) echo -e "\n$help";exit 1;;
#*) echo -e "\nÈ stata inserita un'opzione non valida.\n\n $help";exit 1;;
esac
done
function exit_verify()
{
if [ ${?} -eq 0 ]
then
true
else
exit 1
fi
}
echo " #####################################################"
echo " # #"
echo " # ITSoneDB upgrade program #"
echo " # ETL_population_pipeline #"
echo " # #"
echo " #####################################################"
echo ""
echo ""
echo ""
scripts=`realpath -s {scripts}`
releases=`realpath -s {releases}`
echo $scripts
#x) aux=${OPTARG};;
echo $release
echo $releases
echo $prevrel
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/0_splitter.py
-t ${releases}/${release}/tsv_${release}/
-f ${releases}/${release}/fasta_${release}/
-i ${releases}/${release}/ITS1_loc_final_table.csv
-o ${releases}/${release}/etl"
${scripts}/0_splitter.py\
-t ${releases}/${release}/tsv_${release}/\
-f ${releases}/${release}/fasta_${release}/\
-i ${releases}/${release}/ITS1_loc_final_table.csv\
-o ${releases}/${release}/etl
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/1_correct_final_table_taxid.py
-i ${releases}/${release}/ITS1_loc_final_table.csv
-t ${releases}/${release}/taxonomy_${release}
-m ${releases}/${release}/excluded_ITS1_ENA.csv
-p ${releases}/${prevrel}/taxonomy_${prevrel}
-o ${releases}/${release}/etl"
${scripts}/1_correct_final_table_taxid.py\
-i ${releases}/${release}/ITS1_loc_final_table.csv\
-t ${releases}/${release}/taxonomy_${release}\
-m ${releases}/${release}/excluded_ITS1_ENA.csv\
-p ${releases}/${prevrel}/taxonomy_${prevrel}\
-o ${releases}/${release}/etl
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/2_create_mapping_ENA_ITSoneDB_acc.py
-i ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv
-o ${releases}/${release}/etl
-r ${release}
-f ${releases}/${release}/etl/acc2fasta_info.csv.gz
-m ${releases}/${prevrel}/etl/mapping_data_ENA_release_${prevrel}.tsv
-n ${releases}/${release}/taxonomy_${release}"
${scripts}/2_create_mapping_ENA_ITSoneDB_acc.py\
-i ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv\
-o ${releases}/${release}/etl\
-r ${release}\
-f ${releases}/${release}/etl/acc2fasta_info.csv.gz\
-m ${releases}/${prevrel}/etl/mapping_data_ENA_release_${prevrel}.tsv\
-n ${releases}/${release}/taxonomy_${release}
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/3_prepare_gbentry.py
-i ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv
-f ${releases}/${release}/etl/acc2fasta_info.csv.gz
-t ${releases}/${release}/etl/acc2tsv_info.csv.gz
-o ${releases}/${release}/etl"
${scripts}/3_prepare_gbentry.py\
-i ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv\
-f ${releases}/${release}/etl/acc2fasta_info.csv.gz\
-t ${releases}/${release}/etl/acc2tsv_info.csv.gz\
-o ${releases}/${release}/etl
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/4_Alignment_splitter.py
-m ${releases}/${release}/ITS1_loc_NHMMER.csv
-a ${releases}/${release}/align_${release}
-r ${release}
-o ${releases}/${release}/etl"
${scripts}/4_Alignment_splitter.py\
-m ${releases}/${release}/ITS1_loc_NHMMER.csv\
-a ${releases}/${release}/align_${release}\
-r ${release}\
-o ${releases}/${release}/etl
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/5_prepare_flanking_region.py
-m ${releases}/${release}/etl/mapping_data_ENA_release_${release}.tsv
-b ${releases}/${release}/ITS1_loc_NHMMER.csv
-f ${releases}/${release}/etl/hmm_match_data/alignment_18S
-r ${releases}/${release}/etl/hmm_match_data/alignment_5_8S
-a ${releases}/${release}/etl/acc2fasta_info.csv.gz
-o ${releases}/${release}/etl"
${scripts}/5_prepare_flanking_region.py\
-m ${releases}/${release}/etl/mapping_data_ENA_release_${release}.tsv\
-b ${releases}/${release}/ITS1_loc_NHMMER.csv\
-f ${releases}/${release}/etl/hmm_match_data/alignment_18S\
-r ${releases}/${release}/etl/hmm_match_data/alignment_5_8S\
-a ${releases}/${release}/etl/acc2fasta_info.csv.gz\
-o ${releases}/${release}/etl
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/6_find_representative.py
-f ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}.fa.gz
-n ${releases}/${release}/taxonomy_${release}
-o ${releases}/${release}/etl
-p 20"
${scripts}/6_find_representative.py\
-f ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}.fa.gz\
-n ${releases}/${release}/taxonomy_${release}\
-o ${releases}/${release}/etl\
-p 20
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/7_rep_fasta_generation.py
-r ${release}
-c ${releases}/${release}/etl/Representative_computation/rep_sequences.csv
-i ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}.fa.gz
-f ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}_with_flanking.fa
-o ${releases}/${release}/etl/Representative_computation"
${scripts}/7_rep_fasta_generation.py\
-r ${release}\
-c ${releases}/${release}/etl/Representative_computation/rep_sequences.csv\
-i ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}.fa.gz\
-f ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}_with_flanking.fa.gz\
-o ${releases}/${release}/etl/Representative_computation
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/8_taxonomy_cleaner.py
-n ${releases}/${release}/taxonomy_${release}
-l ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv
-o ${releases}/${release}/etl"
${scripts}/8_taxonomy_cleaner.py\
-n ${releases}/${release}/taxonomy_${release}\
-l ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv\
-o ${releases}/${release}/etl
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/9_prepare_fasta_input.py
-m ${releases}/${release}/etl/mapping_data_ENA_release_${release}.tsv
-f ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}.fa.gz
-n ${releases}/${release}/etl/cleaned_ncbi_taxonomy
-o ${releases}/${release}/etl/FASTA_STATICI"
${scripts}/9_prepare_fasta_input.py\
-m ${releases}/${release}/etl/mapping_data_ENA_release_${release}.tsv\
-f ${releases}/${release}/etl/FASTA_STATICI/ITSoneDB_total_fasta_rel${release}.fa.gz\
-n ${releases}/${release}/etl/cleaned_ncbi_taxonomy\
-o ${releases}/${release}/etl/FASTA_STATICI
exit_verify
echo ""
echo ""
echo "############################################################################################"
echo "${scripts}/10_prepare_its1feauture_file.py
-i ${releases}/${release}/etl/mapping_data_ENA_release_${release}.tsv
-l ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv
-o ${releases}/${release}/etl"
${scripts}/10_prepare_its1feauture_file.py\
-i ${releases}/${release}/etl/mapping_data_ENA_release_${release}.tsv\
-l ${releases}/${release}/etl/ITS1_loc_final_table_corrected.tsv\
-o ${releases}/${release}/etl
exit_verify