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RFSC.sh
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#!/bin/bash
#
#####################################################################
# ================================================================= #
# = = #
# = R F S C = #
# = = #
# = A Reference-Free Sequence Classification Tool = #
# = for DNA sequences in metagenomic samples. = #
# = = #
# ================================================================= #
#####################################################################
#
SHOW_HELP=0;
SHOW_VERSION=0;
INSTALL=0;
CLEAN=0;
CLEAN_ALL=0;
#
BUILD_DB_VIRUS=0;
BUILD_DB_BACTERIA=0;
BUILD_DB_ARCHAEA=0;
BUILD_DB_PROTOZOA=0;
BUILD_DB_FUNGI=0;
BUILD_DB_PLANT=0;
#BUILD_DB_INVERTEBRATE=0;
#BUILD_DB_VERTEBRATE_MAMMALIAN=0;
#BUILD_DB_VERTEBRATE_OTHER=0;
BUILD_DB_MITOCHONDRIAL=0;
BUILD_DB_PLASTID=0;
#
GEN_ADAPTERS=0;
#
THREADS_AVAILABLE=`cat /proc/cpuinfo | awk '/^processor/{print $3}' | wc -l`;
THREADS=0;
GET_THREADS="";
#
SET_THRESHOLD_REF_BASED=0;
MAX_THRESHOLD_REF_BASED=70;
MIN_THRESHOLD_REF_BASED=1;
GET_MAX_THRESHOLD_REF_BASED="";
GET_MIN_THRESHOLD_REF_BASED="";
#
GEN_SYNTHETIC=0;
REF_FILE1="";
REF_FILE2="";
REF_FILE3="";
REF_FILE4="";
LAST_MIX=0;
#
CRYFA_FLAG=0;
#
TRIMMING_FLAG=0;
TRIMMING_TYPE="";
TRIMMING_THREADS=0;
TRIMMING_MODE=""; # SE or PE
#
ASSEMBLY_FLAG=0;
#
SET_LEN_COV=0;
NODE_LENGTH=100;
NODE_COVERAGE=3;
SET_NODE_LENGTH="";
SET_NODE_COVERAGE="";
#
FALCON_FLAG=0;
FALCON_MODE="";
FALCON_DOMAIN="";
FALCON_TARGET_DOMAIN="DB-viral" # Default
BLASTN_REMOTE_FLAG=0;
#
RUN_DECRYPT=0;
RUN_ENCRYPT=0;
#
ORFFINDER_FLAG=0;
#
ORF_DATASETS=0;
ORF_TOOL="";
ORF_DOMAIN="";
#
NC_DNA_FLAG=0;
NC_DNA_DOMAIN="";
#
NC_AA_FLAG=0;
NC_AA_DOMAIN="";
#
GC_CONTENT_FLAG=0;
GC_CONTENT_DOMAIN="";
#
LEN_SEQ_FLAG=0;
LEN_SEQ_DOMAIN="";
#
EFETCH_FLAG=0;
EFETCH_ID="";
EFETCH_FOLDER="";
#
TRAIN_TEST_DATASET_FLAG=0;
TRAIN_TEST_DATASET_PARTITION="";
#
LIMIT_SAMPLES_DATASET_FLAG=0;
LIMIT_SAMPLES_DATASET="";
#
RUN_GNB=0;
NUM_DOMAINS="";
PREDICTORS_CODE="";
#
RUN_KNN=0;
KNN_K="";
#
RUN_XGB=0;
#
TEST_KNN_FLAG=0;
TEST_KNN_MODE="";
#
TEST_XGB_FLAG=0;
TEST_XGB_MODE="";
#
TEST_GNB_CV_FLAG=0;
TEST_GNB_DOMAIN="";
#
TEST_GNB_FLAG=0;
TEST_GNB_TRAIN_PERCENTAGE="";
#
ACCURACY_KNN_FLAG=0;
ACCURACY_KNN_MODE="";
ACCURACY_KNN_TRAIN="";
#
ACCURACY_XGB_FLAG=0;
ACCURACY_XGB_MODE="";
ACCURACY_XGB_TRAIN="";
#
ACCURACY_GNB_FLAG=0;
ACCURACY_GNB_MODE="";
ACCURACY_GNB_TRAIN="";
ACCURACY_GNB_TRAIN_PERC="";
#
#
# ==================================================================
# VERIFICATION FUNCTIONS
#
CHECK_ADAPTERS() {
if [ ! -f Input_Data/ReferenceBased/adapters.fa ]; then
echo -e "\033[1;33m[RFSC] ERROR: adapter sequences (adapter.fa) not found! \033[0m"
echo -e "\033[1;34m[RFSC] \033[0;33m ./RFSC.sh --gen-adapters \033[0m : To generate the adapter sequences ...";
fi
}
#
# ==================================================================
# GENERATE SYNTHETIC SEQUENCE
#
GENERATE_SYNTHETIC () {
./src/SyntheticGenerator/mixRefs.sh "$REF_FILE1" "$REF_FILE2" "$REF_FILE3";
LAST_MIX=$( ls src/SyntheticGenerator/Inputs/ | wc -l )
./src/SyntheticGenerator/syntheticGen.sh src/SyntheticGenerator/Inputs/"mix${LAST_MIX}.fa";
}
#
# ==================================================================
# TRIMMING/FILTERING SEQUENCES
#
TRIMMING_SEQUENCE() {
#
# Fetch the input files
i=0;
for file in Input_Data/ReferenceBased/*.fq.gz
do
input_file[i]="$file"
(( i++ ))
done
#
if [[ $TRIMMING_TYPE == "TT" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m Trimming using Trimmomatic";
TRIMMING_THREADS=$THREADS_AVAILABLE;
echo -e "\033[1;34m[RFSC]\033[0m Currently using $TRIMMING_THREADS available threads!";
#
CHECK_ADAPTERS;
cp Input_Data/ReferenceBased/adapters.fa adapters.fa
#
if [[ $TRIMMING_MODE == "PE" ]]; then
trimmomatic $TRIMMING_MODE -threads $TRIMMING_THREADS -phred33 ${input_file[0]} ${input_file[1]} GeneratedFiles/o_fw_pr.fq GeneratedFiles/o_fw_unpr.fq GeneratedFiles/o_rv_pr.fq GeneratedFiles/o_rv_unpr.fq ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
elif [[ $TRIMMING_MODE == "SE" ]]; then
trimmomatic $TRIMMING_MODE -threads $TRIMMING_THREADS -phred33 ${input_file[0]} GeneratedFiles/out.fq ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
else
echo -e "\033[1;34m[RFSC] \033[1;31m Invalid Argument - $TRIMMING_MODE! \033[0m";
echo -e "\033[1;34m[RFSC]\033[0m Use one of the follow:";
echo -e "\033[1;34m[RFSC] \033[0;33m PE \033[0m : To use paired end reads";
echo -e "\033[1;34m[RFSC] \033[0;33m SE \033[0m : To use single end reads";
exit 0;
fi
#
rm adapters.fa
#
elif [[ $TRIMMING_TYPE == "FP" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m Trimming with FASTP";
#
if [[ $TRIMMING_MODE == "PE" ]]; then
fastp -i ${input_file[0]} -I ${input_file[1]} -o GeneratedFiles/out1.fq.gz -O GeneratedFiles/out2.fq.gz
elif [[ $TRIMMING_MODE == "SE" ]]; then
fastp -i ${input_file[0]} -o GeneratedFiles/out.fq.gz
else
echo -e "\033[1;34m[RFSC] \033[1;31m Invalid Argument - $TRIMMING_MODE! \033[0m";
echo -e "\033[1;34m[RFSC]\033[0m Use one of the follow:";
echo -e "\033[1;34m[RFSC] \033[0;33m PE \033[0m : To use paired end reads";
echo -e "\033[1;34m[RFSC] \033[0;33m SE \033[0m : To use single end reads";
exit 0;
fi
#
mv fastp.html Outputs/
mv fastp.json Outputs/
else
echo -e "\033[1;34m[RFSC] \033[1;31m Invalid Argument - $TRIMMING_TYPE! \033[0m";
echo -e "\033[1;34m[RFSC]\033[0m Use one of the follow:";
echo -e "\033[1;34m[RFSC] \033[0;33m TT \033[0m : To use the Trimmomatic Tool";
echo -e "\033[1;34m[RFSC] \033[0;33m FP \033[0m : To use the FASTP Tool";
exit 0;
fi
}
#
# ==================================================================
# DE-NOVO ASSEMBLY
#
SPADES_ASSEMBLY() {
if [[ $TRIMMING_TYPE == "TT" ]]; then
if [[ $TRIMMING_MODE == "PE" ]]; then
spades.py -t 16 --careful -o GeneratedFiles/out_spades_$1 -1 GeneratedFiles/o_fw_pr.fq -2 GeneratedFiles/o_rv_pr.fq -s GeneratedFiles/o_fw_unpr.fq -s GeneratedFiles/o_rv_unpr.fq
else
spades.py -t 16 --careful -o GeneratedFiles/out_spades_$1 -s GeneratedFiles/out.fq
fi
else
if [[ $TRIMMING_MODE == "PE" ]]; then
spades.py -t 16 --careful -o GeneratedFiles/out_spades_$1 -1 GeneratedFiles/out1.fq.gz -2 GeneratedFiles/out2.fq.gz
else
spades.py -t 16 --careful -o GeneratedFiles/out_spades_$1 -s GeneratedFiles/out.fq.gz
fi
fi
}
#
# ==================================================================
# PARSE SCAFFOLDS INTO NODES (MINOR SCAFFOLDS)
#
PARSE_SCAFFOLDS() {
echo -e "\033[1;34m[RFSC]\033[0m Start parsing scaffolds.fasta"
mkdir GeneratedFiles/out_spades_/Nodes
awk '/>/{filename="GeneratedFiles/out_spades_/Nodes/"NR".fasta"}; {print >filename}' GeneratedFiles/out_spades_/scaffolds.fasta
echo -e "\033[1;34m[RFSC]\033[0m Parse finnished! The result can be find in GeneratedFiles/out_spades_/Nodes/"
echo -e "\033[1;34m[RFSC]\033[0m Start filtering nodes based on Lenght & Coverage!"
for file in GeneratedFiles/out_spades_/Nodes/*
do
REF=`grep ">" < $file`
NODE_LEN=$(awk -F_ '{print $4}' <<< ${REF})
NODE_COV=$(awk -F_ '{print $6}' <<< ${REF})
COV_TO_INT=(${NODE_COV//./ })
if [[ "$NODE_LEN" -gt "$NODE_LENGTH" ]] && [[ "${COV_TO_INT[0]}" -ge "$NODE_COVERAGE" ]]; then
continue
else
rm $file
echo -e "\033[1;34m[RFSC]\033[0m $file Node has been removed in the filtering process!"
fi
done
}
#
# ==================================================================
# FALCON ANALYSIS - SELECT DOMAIN
#
FALCON_SELECT_DOMAIN() {
if [[ "$FALCON_DOMAIN" == "Viral" ]]; then
FALCON_TARGET_DOMAIN="DB-viral"
if [[ ! -f "References/NCBI-Virus/DB-viral.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-viral.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Bacteria" ]]; then
FALCON_TARGET_DOMAIN="DB-bacteria"
if [[ ! -f "References/NCBI-Bacteria/DB-bacteria.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-bacteria.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Archaea" ]]; then
FALCON_TARGET_DOMAIN="DB-archaea"
if [[ ! -f "References/NCBI-Archaea/DB-archaea.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-archaea.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Fungi" ]]; then
FALCON_TARGET_DOMAIN="DB-fungi"
if [[ ! -f "References/NCBI-Fungi/DB-fungi.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-fungi.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Plant" ]]; then
FALCON_TARGET_DOMAIN="DB-plant"
if [[ ! -f "References/NCBI-Plant/DB-plant.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-plant.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Protozoa" ]]; then
FALCON_TARGET_DOMAIN="DB-protozoa"
if [[ ! -f "References/NCBI-Protozoa/DB-protozoa.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-protozoa.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Mitochondrial" ]]; then
FALCON_TARGET_DOMAIN="DB-mitochondrion"
if [[ ! -f "References/NCBI-Mitochondrial/DB-mitochondrion.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-mitochondrion.fa was not found! Aborting..."
exit 0
fi
elif [[ "$FALCON_DOMAIN" == "Plastid" ]]; then
FALCON_TARGET_DOMAIN="DB-plastid"
if [[ ! -f "References/NCBI-Plastid/DB-plastid.fa" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m DB-plastid.fa was not found! Aborting..."
exit 0
fi
else
echo -e "\033[1;34m[RFSC]\033[0m $FALCON_DOMAIN not recognized! Please select a valid domain from the next ones:"
echo -e "\033[1;34m[RFSC]\033[0m Viral | Bacteria | Archaea | Fungi | Plant | Protozoa | Mitochondrial | Plastid"
exit 0
fi
}
#
# ==================================================================
# FALCON ANALYSIS - SCAFFOLDS
#
FALCON_SO_MODE() {
FALCON_SELECT_DOMAIN;
FALCON -n $THREADS_AVAILABLE -v -F -x Outputs/falcon_SO_results.txt GeneratedFiles/out_spades_/scaffolds.fasta References/NCBI-Virus/$FALCON_TARGET_DOMAIN.fa
echo -e "\033[1;34m[RFSC]\033[0m Outputs/falcon_SO_results.txt file was successfully been generated!"
#
readarray -t results <Outputs/falcon_SO_results.txt
#
NUM_RES=${#results[@]}
for (( i=0; i<$NUM_RES; i++ ));
do
VIRUS=`echo "${results[i]}"|awk 'NF>1{print $NF}'`
PER=`echo "${results[i]}"|awk '{print $3}'`
BOOL=`echo "$PER > 70.000" | bc`
#
if [[ $BOOL -eq "1" ]]; then
printf "$VIRUS\n" >> Results/ref_result.txt
fi
done
}
#
# ==================================================================
# FALCON ANALYSIS - EACH READS
#
FALCON_RM_MODE() {
FALCON_SELECT_DOMAIN;
reads=0
for file in GeneratedFiles/out_spades_/Nodes/*
do
array[ $reads ]=$file
(( reads++ ))
done
#
mkdir Outputs/FalconNodes
len=${#array[@]}
i=0
while [[ $i != $len ]]
do
if [[ $(( ($len - $i) % 2)) == 0 ]]; then
path1=${array[i]}
path2=${array[i+1]}
path_to_file1=(${path1//// })
path_to_file2=(${path2//// })
R1=${path_to_file1[3]}
R2=${path_to_file2[3]}
echo -e "\033[1;34m[RFSC]\033[0m Analysing Nodes $R1 & $R2 with $(($THREADS_AVAILABLE/2)) threads each!"
FALCON -n $(($THREADS_AVAILABLE/2)) -v -F -x Outputs/FalconNodes/falcon_RM_"${R1}"_results.txt GeneratedFiles/out_spades_/Nodes/$R1 References/NCBI-Virus/$FALCON_TARGET_DOMAIN.fa | FALCON -n $(($THREADS_AVAILABLE/2)) -v -F -x Outputs/FalconNodes/falcon_RM_"${R2}"_results.txt GeneratedFiles/out_spades_/Nodes/$R2 References/NCBI-Virus/$FALCON_TARGET_DOMAIN.fa
(( i+=2 ))
else
path=${array[i]}
path_to_file=(${path//// })
R=${path_to_file[3]}
echo -e "\033[1;34m[RFSC]\033[0m Analysing Node $R with $(($THREADS_AVAILABLE)) threads!"
FALCON -n $(($THREADS_AVAILABLE)) -v -F -x Outputs/FalconNodes/falcon_RM_"${R}"_results.txt GeneratedFiles/out_spades_/Nodes/$R References/NCBI-Virus/$FALCON_TARGET_DOMAIN.fa
(( i++ ))
fi
done
}
#
# ==================================================================
# SELECT RESULTS (AFTER FALCON)
#
SELECT_RESULTS() {
echo -e "\033[1;34m[RFSC]\033[0m Starting selection procedure"
mkdir Results/falcon_seq
for file in Outputs/FalconNodes/*
do
readarray -t fasta_node <$file
NLINES=${#fasta_node[@]}
for (( i=0; i<$NLINES; i++ ));
do
PER=`echo "${fasta_node[i]}"|awk '{print $3}'`
FIND_MATCH=`echo "$PER > $MAX_THRESHOLD_REF_BASED" | bc`
SECOND_PHASE=`echo "$PER > $MIN_THRESHOLD_REF_BASED && $PER < $MAX_THRESHOLD_REF_BASED" | bc`
file=${file#"Outputs/FalconNodes/falcon_RM_"}
file=${file%"_results.txt"}
if [[ $FIND_MATCH -eq "1" ]]; then
GENOME=`echo "${fasta_node[i]}"|awk '{print $4}'`
echo -e "\033[1;34m[RFSC]\033[0m Moving $file to Results/falcon_seq"
mv GeneratedFiles/out_spades_/Nodes/$file Results/falcon_seq
ALREADY_FOUND=`grep -x $GENOME Results/ref_result.txt`
if [[ $ALREADY_FOUND != "" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m Sequence already stated in Results/ref_result.txt"
else
printf "$GENOME\n" >> Results/ref_result.txt
fi
break
elif [[ $SECOND_PHASE -eq "1" ]]; then
echo -e "\033[1;34m[RFSC]\033[0m Moving $file to Input_Data/ReferenceFree"
mv GeneratedFiles/out_spades_/Nodes/$file Input_Data/ReferenceFree
break
else
echo -e "\033[1;34m[RFSC]\033[0m Deleting $file"
rm GeneratedFiles/out_spades_/Nodes/$file
break
fi
done
done
}
#
# ==================================================================
# FALCON ANALYSIS
#
FALCON_ANALYSIS() {
if [[ $FALCON_MODE == "SO" ]]; then
FALCON_SO_MODE;
elif [[ $FALCON_MODE == "RM" ]]; then
FALCON_SO_MODE;
PARSE_SCAFFOLDS;
FALCON_RM_MODE;
SELECT_RESULTS;
else
echo -e "\033[1;34m[RFSC] \033[1;31m Invalid Argument - $FALCON_MODE! \033[0m";
echo -e "\033[1;34m[RFSC]\033[0m Use one of the follow:";
echo -e "\033[1;34m[RFSC] \033[0;33m SO \033[0m : To analyse only the scaffold";
echo -e "\033[1;34m[RFSC] \033[0;33m RM \033[0m : To use redundancy in the analyse (Run each Read)";
exit 0;
fi
}
#
# ==================================================================
# BLASTN ANALYSIS
#
BLASTN_ANALYSIS() {
PARSE_SCAFFOLDS;
mkdir Outputs/BlastnNodes
for file in GeneratedFiles/out_spades_/Nodes/*
do
file_name=$(basename $file);
echo -e "\033[1;34m[RFSC]\033[0m Blastn is now processing $file"
blastn -db nt -task blastn-short -query $file -remote > Outputs/BlastnNodes/$file_name.txt
done
}
#
# ==================================================================
# ORF FINDER SEARCH (ORFfinder)
#
ORF_SEARCH() {
mkdir ORFs/NodesProteins
for file in Input_Data/ReferenceFree/*
do
node_file=$(basename $file);
echo -e "\033[1;34m[RFSC]\033[0m ORFfinder is now processing $node_file"
node_file=${node_file%".fasta"}
./ORFs/ORFfinder -s 1 -in Input_Data/ReferenceFree/$node_file.fasta -outfmt 0 -out ORFs/NodesProteins/$node_file.protein.fasta
done
}
#
# ==================================================================
# ENCRYPTION
#
ENCRYPT_DATA() {
echo -e "\033[1;34m[RFSC]\033[0;32m Please insert the password to encrypt the files contained in /Data_Security/Encrypt_Input: \033[0m";
read -s password
echo "$password" > key.txt
#
for file in Data_Security/Encrypt_Input/*
do
echo -e "\033[1;34m[RFSC]\033[0;32m Encrypting $file ... \033[0m";
out_file=$(basename $file);
cryfa -k key.txt $file > Data_Security/Encrypted_Data/$out_file.enc
done
rm -f key.txt
echo -e "\033[1;34m[RFSC]\033[0;32m $file has been encrypted! \033[0m";
}
#
# ==================================================================
# DECRYPTION
#
DECRYPT_DATA() {
for file in Data_Security/Encrypted_Data/*
do
echo -e "\033[1;34m[RFSC]\033[0;32m Decrypting $file ... \033[0m";
out_file=$(basename $file);
echo -e "\033[1;34m[RFSC]\033[0;32m Please insert the password to decrypt the file $file: \033[0m";
read -s password
echo "$password" > key.txt
cryfa -k key.txt -d $file > Data_Security/Decrypted_Data/$out_file.dec;
echo -e "\033[1;34m[RFSC]\033[0;32m $file has been decrypted! \033[0m";
rm -f key.txt;
done
}
#
# ==================================================================
# OPTIONS
#
if [ "$#" -eq 0 ]; then
SHOW_HELP=1;
fi
#
POSITIONAL=();
#
while [[ $# -gt 0 ]]
do
i="$1";
case $i in
-h|--help|?)
SHOW_HELP=1;
shift
;;
-v|-V|--version)
SHOW_VERSION=1;
shift
;;
-i|--install)
INSTALL=1;
shift
;;
-t|--threads)
THREADS=1;
GET_THREADS="$2";
shift 2
;;
-tmm|--set-threshold-max-min)
SET_THRESHOLD_REF_BASED=1;
GET_MAX_THRESHOLD_REF_BASED="$2";
GET_MIN_THRESHOLD_REF_BASED="$3";
shift 3
;;
-dlc|--set-len-cov)
SET_LEN_COV=1;
SET_NODE_LENGTH="$2";
SET_NODE_COVERAGE="$3";
shift 3
;;
-bviral|--build-ref-virus)
BUILD_DB_VIRUS=1;
shift
;;
-bbact|--build-ref-bacteria)
BUILD_DB_BACTERIA=1;
shift
;;
-barch|--build-ref-archaea)
BUILD_DB_ARCHAEA=1;
shift
;;
-bprot|--build-ref-protozoa)
BUILD_DB_PROTOZOA=1;
shift
;;
-bfung|--build-ref-fungi)
BUILD_DB_FUNGI=1;
shift
;;
-bplan|--build-ref-plant)
BUILD_DB_PLANT=1;
shift
;;
-bmito|--build-ref-mitochondrial)
BUILD_DB_MITOCHONDRIAL=1;
shift
;;
-bplas|--build-ref-plastid)
BUILD_DB_PLASTID=1;
shift
;;
-gad|--gen-adapters)
GEN_ADAPTERS=1;
shift
;;
-synt|--synthetic)
GEN_SYNTHETIC=1;
REF_FILE1="$2";
REF_FILE2="$3";
REF_FILE3="$4";
shift 4
;;
-trim|--filter)
TRIMMING_FLAG=1;
TRIMMING_TYPE="$2";
TRIMMING_MODE="$3";
shift 3
;;
-rda|--run-de-novo)
ASSEMBLY_FLAG=1;
shift
;;
-rfa|--run-falcon)
FALCON_FLAG=1;
FALCON_MODE="$2";
FALCON_DOMAIN="$3"
shift 3
;;
-rbr|--run-blastn-remote)
BLASTN_REMOTE_FLAG=1;
shift
;;
-orf|--orf-finder)
ORFFINDER_FLAG=1;
shift
;;
-orfd|--orf-dataset)
ORF_DATASETS=1;
ORF_TOOL="$2";
ORF_DOMAIN="$3";
shift 3
;;
-enc|--encrypt)
RUN_ENCRYPT=1;
shift
;;
-dec|--decrypt)
RUN_DECRYPT=1;
shift
;;
-ball|--build-ref-all)
BUILD_DB_VIRUS=1;
BUILD_DB_BACTERIA=1;
BUILD_DB_ARCHAEA=1;
BUILD_DB_PROTOZOA=1;
BUILD_DB_FUNGI=1;
BUILD_DB_PLANT=1;
BUILD_DB_INVERTEBRATE=1;
BUILD_DB_VERTEBRATE_MAMMALIAN=1;
BUILD_DB_VERTEBRATE_OTHER=1;
BUILD_DB_MITOCHONDRIAL=1;
BUILD_DB_PLASTID=1;
shift
;;
-ncd|--nc-dna-csv)
NC_DNA_FLAG=1;
NC_DNA_DOMAIN="$2";
shift 2
;;
-nca|--nc-aa-csv)
NC_AA_FLAG=1;
NC_AA_DOMAIN="$2";
shift 2
;;
-gc|--gc-content-csv)
GC_CONTENT_FLAG=1;
GC_CONTENT_DOMAIN="$2";
shift 2
;;
-lenseq|--len-dna-aa-csv)
LEN_SEQ_FLAG=1;
LEN_SEQ_DOMAIN="$2";
shift 2
;;
-efetch|--efetch-fasta)
EFETCH_FLAG=1;
EFETCH_ID="$2";
EFETCH_FOLDER="$3";
shift 3
;;
-train-test|--train-test-dataset-csv)
TRAIN_TEST_DATASET_FLAG=1;
TRAIN_TEST_DATASET_PARTITION="$2";
shift 2
;;
-sdataset|--small-dataset-csv)
LIMIT_SAMPLES_DATASET_FLAG=1;
LIMIT_SAMPLES_DATASET="$2";
shift 2
;;
-gnb|--run-gaussian-naive-bayes-classifier)
RUN_GNB=1;
NUM_DOMAINS="$2";
PREDICTORS_CODE="$3";
shift 3
;;
-knn|--run-k-nearest-neighbor-classifier)
RUN_KNN=1;
KNN_K="$2";
shift 2
;;
-xgb|--run-xgboost)
RUN_XGB=1;
shift
;;
-testKNN)
TEST_KNN_FLAG=1;
TEST_KNN_MODE="$2";
shift 2
;;
-testXGB)
TEST_XGB_FLAG=1;
TEST_XGB_MODE="$2";
shift 2
;;
-testGNB)
TEST_GNB_FLAG=1;
TEST_GNB_TRAIN_PERCENTAGE="$2";
shift 2
;;
-testGNB-CV|--testGNB-CrossV)
TEST_GNB_CV_FLAG=1;
TEST_GNB_DOMAIN="$2";
shift 2
;;
-aKNN|--accuracy-KNN)
ACCURACY_KNN_FLAG=1;
ACCURACY_KNN_MODE="$2";
ACCURACY_KNN_TRAIN="$3";
shift 3
;;
-aXGB|--accuracy-XGB)
ACCURACY_XGB_FLAG=1;
ACCURACY_XGB_MODE="$2";
ACCURACY_XGB_TRAIN="$3";
shift 3
;;
-aGNB|--accuracy-GNB)
ACCURACY_GNB_FLAG=1;
ACCURACY_GNB_MODE="$2";
ACCURACY_GNB_TRAIN="$3";
ACCURACY_GNB_TRAIN_PERC="$4"
shift 4
;;
-clc|--clean)
CLEAN=1;
shift
;;
-cla|--clean-all)
CLEAN_ALL=1;
shift
;;
-all|--run-all)
CLEAN=1;
SET_THRESHOLD_REF_BASED=1;
GET_MAX_THRESHOLD_REF_BASED="70";
GET_MIN_THRESHOLD_REF_BASED="1";
SET_LEN_COV=1;
SET_NODE_LENGTH="100";
SET_NODE_COVERAGE="3";
TRIMMING_FLAG=1;
TRIMMING_TYPE="TT";
TRIMMING_MODE="PE";
ASSEMBLY_FLAG=1;
FALCON_FLAG=1;
FALCON_MODE="RM";
FALCON_DOMAIN="Viral";
RUN_KNN=1;
KNN_K="2";
shift
;;
-*) # Unknown option
echo -e "\033[1;34m[RFSC] \033[1;31m Invalid arg ($1)! \033[0m";
echo -e "\033[1;34m[RFSC]\033[0m For more help, try: \033[0;33m./RFSC.sh -h \033[0m"
exit 1;
;;
esac
done
#
set -- "${POSITIONAL[@]}" # Restore positional parameters
#
# ======================================================================
# HELP MENU
#
if [ "$SHOW_HELP" -eq "1" ]; then
echo " "
echo -e " \033[0;36m ____ _____ ____ ____ \033[0m "
echo -e " \033[0;36m | _ \| ___/ ___| / ___| \033[0m "
echo -e " \033[0;36m | |_) | |_ \___ \| | \033[0m "
echo -e " \033[0;36m | _ <| _| ___) | |___ \033[0m "
echo -e " \033[0;36m |_| \_\_| |____/ \____| \033[0m "
echo " "
echo -e " \033[1;34m P I P E L I N E \033[0m "
echo " "
echo -e " \033[3;34m A Reference-Free Sequence Classification Tool \033[0m "
echo -e " \033[3;34m for DNA sequences in metagenomic samples. \033[0m "
echo " "
echo -e " \033[1;33m Usage: ./RFSC.sh [options] \033[0m "
echo " "
echo " -h, --help Show this help message and exit "
echo " -v, --version Show the version and some information "
echo " -i, --install Installation of all the needed tools "
echo " "
echo -e " -t, --threads \033[0;34m<THREADS>\033[0m "
echo " Number of threads to be used "
echo " "
echo " -dec, --decrypt Decrypt all files in /Data_Security/Decrypted_Data "
echo " -enc, --encrypt Encrypt all files in /Data_Security/Encrypted_data "
echo " "
echo -e " -tmm, --set-threshold-max-min \033[0;34m<MAX> <MIN>\033[0m "
echo " Set Max & Min thresholds for percentage "
echo " similarity in reference based analysis "
echo " "
echo -e " -dlc, --set-len-cov \033[0;34m<LEN> <COV>\033[0m "
echo " Define the Length and Coverage values "
echo " for the scaffolds filtering process "
echo " "
echo " -gad, --gen-adapters Generate FASTA file with adapters "
echo " "
echo -e " -synt, --synthetic \033[0;34m[FILE1]:[FILE3]\033[0m "
echo " Generate a synthetical sequence using 3 "
echo " reference files for testing purposes "
echo " "
echo -e " -trim, --filter \033[0;34m<TOOL> <MODE>\033[0m "
echo " TOOL: Filter Reads using Trimmomatic (TT) "
echo " or using FASTP (FP) "
echo " MODE: Paired End Reads (PE) "
echo " or Single End Reads (SE) "
echo " "
echo " -rda, --run-de-novo De-Novo Sequence Assembly "
echo " "
echo " -orf, --orf-finder Perform DNA sequence translation for amino acids, "
echo " finds all open reading frames (ORF) and remove "
echo " stop codons "
echo " "
echo -e " -orfd, --orf-dataset \033[0;34m<TOOL> <DOMAIN> \033[0m "
echo " Converts nucleotide sequences presented in the "
echo " NCBI databases into protein sequences "
echo " TOOL: orfM (-orfm) [DEFAULT] "
echo " or using ORF-Finder (-orffinder) "
echo " DOMAIN: --viral, --bacteria, --archaea, ... "
echo " "
echo -e " -ncd, --nc-dna-csv \033[0;34m<DOMAIN> \033[0m "
echo " Compresses and generates a CSV file for the "
echo " DNA NCBI datasets "
echo " DOMAIN: --viral, --bacteria, --archaea, ... "
echo " "
echo -e " -nca, --nc-aa-csv \033[0;34m<DOMAIN> \033[0m "
echo " Compresses and generates a CSV file for the "
echo " AA NCBI datasets "
echo " DOMAIN: --viral, --bacteria, --archaea, ... "
echo " "
echo -e " -gc, --gc-content-csv \033[0;34m<DOMAIN> \033[0m "
echo " Analyses the percentage of GC-Content in each "
echo " sequece of the choosen NCBI database "
echo " DOMAIN: --viral, --bacteria, --archaea, ... "
echo " "
echo -e " -lenseq, --len-dna-aa-csv \033[0;34m<DOMAIN> \033[0m "
echo " Analyses the Length (DNA & AA) sequences the "
echo " choosen NCBI database "
echo " DOMAIN: --viral, --bacteria, --archaea, ... "
echo " "
echo -e " -efetch, --efetch-fasta \033[0;34m<ID> <FOLDER> \033[0m "
echo " Use entrez efetch to fetch a nucleotide using an ID"
echo " ID: Nucleotide Identifier "
echo " FOLDER: Destination Folder (RefBased or RefFree) "
echo -e " \033[1;33m B U I L D D A T A B A S E S \033[0m "
echo " "
echo " -bviral, --build-ref-virus "
echo -e " Build reference database for \033[1;36mvirus\033[0m from NCBI "
echo " -bbact, --build-ref-bacteria "
echo -e " Build reference database for \033[1;36mbacterias\033[0m from NCBI "
echo " -barch, --build-ref-archaea "
echo -e " Build reference database for \033[1;36marchaeas\033[0m from NCBI "
echo " -bprot, --build-ref-protozoa "
echo -e " Build reference database for \033[1;36mprotozoa\033[0m from NCBI "
echo " -bfung, --build-ref-fungi "
echo -e " Build reference database for \033[1;36mfungi\033[0m from NCBI "
echo " -bplan, --build-ref-plant "
echo -e " Build reference database for \033[1;36mplant\033[0m from NCBI "
echo " -bmito, --build-ref-mitochondrial "
echo -e " Build reference database for \033[1;36mmitochondrial\033[0m from NCBI"
echo " -bplas, --build-ref-plastid "
echo -e " Build reference database for \033[1;36mplastid\033[0m from NCBI "
echo -e " \033[1;33m - - - - - - - - - - - - - - - - - - - - - - \033[0m "
echo " "
echo -e " \033[1;33m R E F E R E N C E B A S E D A P P R O A C H \033[0m "
echo " "
echo -e " -rfa, --run-falcon \033[0;34m<MODE> <DOMAIN> \033[0m "
echo " Run Data Analysis with FALCON "
echo " MODE: Use only scaffolds (SO) or analyse by each "
echo " Read (RM) "
echo " DOMAIN: Select Domain to analyse (Viral, Bacteria) "
echo " Archaea, Fungi, Plant, Plastid, etc. "
echo " "
echo " -rbr, --run-blastn-remote "
echo " Run Data Analysus with Blast+ using remote "
echo " access to NCBI databases "
echo -e " \033[1;33m - - - - - - - - - - - - - - - - - - - - - - \033[0m "
echo " "
echo -e " -train-test, --train-test-dataset-csv \033[0;34m<TRAIN_PARTITION> \033[0m "
echo " Divide the dataset into a train and test dataset "
echo " (Usefull for testing the KNN Classifier) "
echo " TRAIN_PARTITION: value (0..1) for the train partition"
echo " "
echo -e " -sdataset, --small-dataset-csv \033[0;34m<MAX_SAMPLES> \033[0m "
echo " Create a small dataset with a maximum of samples "
echo " for each domain "
echo " MAX_SAMPLES: Maximum samples per domain "
echo " "
echo -e " \033[1;33m R E F E R E N C E F R E E A P P R O A C H \033[0m "
echo " "
echo -e " -gnb, --run-gaussian-naive-bayes-classifier \033[0;34m<NUM_DOMAINS> <PREDICTORS>\033[0m "
echo " NUM_DOMAINS: Number of domains supported "
echo " PREDICTORS: Code regarding the desired predictors: "
echo " '1111' -> All predictors "
echo " '0001' -> Only Nucleotide Compression "
echo " '0010' -> Only AA Compression "
echo " '0011' -> Only GC-Content "
echo " '0100' -> Only DNA Length "
echo " '0101' -> Only AA Length "
echo " '0110' -> DNA & AA Compression "
echo " '0111' -> DNA & AA Compression + GC-Content "
echo " '1000' -> DNA & AA Compression + GC-Content + DNA Length "
echo " '1001' -> DNA & AA Compression + GC-Content + DNA & AA Length"
echo " '1010' -> DNA & AA Compression + DNA & AA Length "
echo " "
echo -e " -knn, --run-k-nearest-neighbor-classifier \033[0;34m<K> \033[0m "
echo " K: Number of neighbors for the classifier "
echo " Recommended: K = 2 "
echo " "
echo " -xgb, --run-xgboost Run Xgboost Classifier "
echo -e " \033[1;33m - - - - - - - - - - - - - - - - - - - - - - \033[0m "
echo " "
echo -e " \033[1;33m T E S T C L A S S I F I E R S P E R F O R M A N C E \033[0m "
echo " "
echo -e " -testKNN \033[0;34m<MODE> \033[0m "
echo " Deep test the KNN Classifier "
echo " MODE: Test Database against Train Database (--test)"
echo " Cross-Validation (--viral, --bacteria, ...) "
echo " "
echo -e " -testXGB \033[0;34m<MODE> \033[0m "
echo " Deep test the XGBoost Classifier "
echo " MODE: Test Database against Train Database (--test)"
echo " Cross-Validation (--viral, --bacteria, ...) "
echo " "
echo -e " -testGNB \033[0;34m<PERCENTAGE> \033[0m "
echo " Deep test the GNB Classifier with Test & Train Datasets "
echo " PERCENTAGE: Value between 0..1 representing the "
echo " percentage of the dataset reserved for "
echo " the training "
echo " "
echo -e " -testGNB-CV, --testGNB-CrossV \033[0;34m<DOMAIN> \033[0m "
echo " Deep test the GNB Classifier with Cross-Validation "
echo " DOMAIN: --viral, --bacteria, --archaea, ... "
echo " "
echo -e " -aKNN, --accuracy-KNN \033[0;34m<AC-MODE> <T-MODE> \033[0m "
echo " Analyse the accuracy of the KNN Classifier when "
echo " testing it against a known dataset "
echo " AC-MODE: Simple Accuracy Mean (Accuracy) "
echo " Weighted F1-Score (F1Score) "
echo " T-MODE: Cross-Validation Method (CV) "
echo " Train-Test Database (Test) "
echo " "
echo -e " -aXGB, --accuracy-XGB \033[0;34m<AC-MODE> <T-MODE> \033[0m "
echo " Analyse the accuracy of the XGB Classifier when "
echo " testing it against a known dataset "
echo " AC-MODE: Simple Accuracy Mean (Accuracy) "
echo " Weighted F1-Score (F1Score) "
echo " T-MODE: Cross-Validation Method (CV) "
echo " Train-Test Database (Test) "
echo " "
echo -e " -aGNB, --accuracy-GNB \033[0;34m<AC-MODE> <T-MODE> <TRAIN-PERCENTAGE> \033[0m "
echo " Analyse the accuracy of the KNN Classifier when "
echo " testing it against a known dataset "
echo " AC-MODE: Simple Accuracy Mean (Accuracy) "
echo " Weighted F1-Score (F1Score) "
echo " T-MODE: Cross-Validation Method (CV) "
echo " Train-Test Database (Test) "
echo " TRAIN-PERCENTAGE: Percentage of the dataset used "
echo " for training purpouses "
echo -e " \033[1;33m - - - - - - - - - - - - - - - - - - - - - - \033[0m "
echo " "
echo " -clc, --clean Clean all generated files (Including Results) "
echo " "
echo -e " -cla, --clean-all \033[1;31m[!!DANGER!!]\033[0m Clean all CSV files \033[1;31m[!!DANGER!!] \033[0m "
echo " "
echo " -all, --run-all Run all the options (considering real data) "
echo " "
exit 1;
fi
#
# ======================================================================
# VERSION
#
if [ "$SHOW_VERSION" -eq "1" ]; then
echo " "
echo " RFSC "
echo " "