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RGBEPP/RGBEPP.sh

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#!/bin/bash
### Environment Setting
pkgver=0.0.1
DirHome=$(pwd)
DirRaw=$DirHome/00_raw
DirQcTrim=$DirHome/01_fastp
DirAssembly=$DirHome/02_spades
DirFasta=$DirHome/03_assemblied
DirMap=$DirHome/04_diamond
DirPre=$DirHome/05_pre
DirSplit=$DirHome/06_split
DirMerge=$DirHome/07_merge
DirAlign=$DirHome/08_macse
PathSplitfsata=/usr/bin/splitfasta-cpp
PathMacse=/usr/share/java/macse.jar
PathSortdiamond=/usr/bin/sortdiamond
ARG_C='scaffolds'
ARG_M=16
ARG_T=8
### Get some arrays
show_help(){
# echo -e "\t\t\t\t\t\t\t\033[0;31mR\033[0m\033[0;92mG\033[0m\033[0;94mB\033[0m \033[0;33mE\033[0m\033[0;94mP\033[0m\033[0;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
echo -e "\t\t\t\t\t\t\t\033[0;47;31mR\033[0m\033[0;47;92mG\033[0m\033[0;47;94mB\033[0m\033[0;47m \033[0m\033[0;47;33mE\033[0m\033[0;47;94mP\033[0m\033[0;47;33mP\033[0m\n\t\t\t\t\tReference Genome based Exon Phylogeny Pipeline\n \
Version: $pkgver\n \
License: GPL-2.0-only\n \
Author: Guoyi Zhang\n \
-c\t--contigs\tcontings type: scaffolds or contigs\n \
-g\t--genes\t\tgene file path\n \
-f\t--functions\tfunctions type (optional): all clean \n \
\t \t\tassembly fasta map pre split merge align\n \
-h\t--help\t\tshow this information\n \
-l\t--list\t\tlist file path\n \
-m\t--memory\tmemory settings (optional, default 16 GB)\n \
-r\t--reference\treference genome path\n \
-t\t--threads\tthreads setting (optional, default 8 threads)\n \
\t--macse\t\tMacse jarfile path\n \
\t--sortdiamond\tsortdiamond file path\n \
\t--splitfasta\tsplitfasta file path\n \
for example: bash $0 -c scaffolds -f all -l list -g genes \ \n \
\t -r reference.aa.fas \n"
}
if [ $# -eq 0 ]; then
show_help
exit 1
else
ARGS=$(getopt -o c:,f:,g:,h,l:,m:,r:,t: --long contigs:,genes:,functions:,help,list:,memory:,reference:,threads:,macse:,sortdiamond:,splitfasta: -n 'RGBEPP.sh' -- "$@")
if [ $? != 0 ]; then
echo "Failed to parse options." >&2
exit 1
fi
eval set -- "$ARGS"
while true; do
case "$1" in
-c|--contigs)
case "$2" in
"") shift 2 ;;
*) ARG_C=$2; shift 2 ;;
esac ;;
-g|--genes)
case "$2" in
"") shift 2 ;;
*) ARG_G=$2; shift 2 ;;
esac ;;
-f|--functions)
case "$2" in
"") shift 2 ;;
*) ARG_F=$2; shift 2 ;;
esac ;;
-h|--help)
show_help
shift ;;
-l|--list)
case "$2" in
"") shift 2 ;;
*) ARG_L=$2; shift 2 ;;
esac ;;
-m|--memory)
case "$2" in
"") shift 2 ;;
*) ARG_M=$2; shift 2 ;;
esac ;;
-r|--reference)
case "$2" in
"") shift 2 ;;
*) ARG_R=$2; shift 2 ;;
esac ;;
-t|--threads)
case "$2" in
"") shift 2 ;;
*) ARG_T=$2; shift 2 ;;
esac ;;
--macse)
case "$2" in
"") shift 2 ;;
*) PathMacse=$2; shift 2 ;;
esac ;;
--sortdiamond)
case "$2" in
"") shift 2 ;;
*) PathSortdiamond=$2; shift 2 ;;
esac ;;
--splitfasta)
case "$2" in
"") shift 2 ;;
*) PathSplitfsata=$2; shift 2 ;;
esac ;;
--)
shift; break ;;
*) echo "Unknown option: $1"
exit 1
;;
esac
done
fi
### Get and check some arguments
check_var() {
local var_name="$1"
local var_value="${!var_name}" # get value
if [ -z "$var_value" ]; then
echo "Error: $var_name is not set or is empty"
exit 1
else
echo "$var_name is set to: $var_value"
case "$var_name" in
"ARG_G")
readarray -t genes < "$var_value"
length_gn=${#genes[@]}
;;
"ARG_L")
readarray -t full_names < "$var_value"
length_fn=${#full_names[@]}
;;
"ARG_F")
check_command "cp"
check_command "cd"
check_command "mv"
check_command "find"
check_command "mkdir"
;;
esac
fi
}
check_path(){
local path_name="$1"
local path_value="${!path_name}" # get value
# expand ~
path_value=$(eval echo "$path_value")
if [ -e "$path_value" ]; then
echo "$path_name exists at: $path_value"
else
echo "Error: $path_name does not exist at: $path_value"
exit 1
fi
}
check_command() {
local cmd_name="$1"
if command -v "$cmd_name" >/dev/null 2>&1; then
echo "$cmd_name command exists."
else
echo "Error: $cmd_name command not found."
exit 1
fi
}
### Quality control && Trimming
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "clean" ]; then
## Prepare
mkdir -p $DirQcTrim
check_var "ARG_L"
check_command "fastp"
readarray -t full_names < "$ARG_L"
length_fn=${#full_names[@]}
readarray -t genes < "$ARG_G"
length_gn=${#genes[@]}
## Quality control and trimming using fastp
for (( i=0; i<$length_fn; i++ )); do
fastp -i $DirRaw/${full_names[$i]}_R1.fastq.gz -I $DirRaw/${full_names[$i]}_R2.fastq.gz -j $DirQcTrim/${full_names[$i]}.json -h $DirQcTrim/${full_names[$i]}.html -o $DirQcTrim/${full_names[$i]}_R1.fastq.gz -O $DirQcTrim/${full_names[$i]}_R2.fastq.gz -w $ARG_T
done
fi
### De novo assembly
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "assembly" ]; then
## Prepare
mkdir -p $DirAssembly
check_var "ARG_L"
check_command "spades.py"
## De novo assembly using spades
for (( i=0; i<$length_fn; i++ )); do
mkdir -p $DirAssembly/${full_names[$i]}
spades.py --pe1-1 $DirQcTrim/${full_names[$i]}_R1.fastq.gz --pe1-2 $DirQcTrim/${full_names[$i]}_R2.fastq.gz -t $ARG_T -m $ARG_M --careful --phred-offset 33 -o $DirAssembly/${full_names[$i]}
# -k 96,107,117,127 \
done
fi
### Moving scaffords or Contigs out
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "fasta" ]; then
## Check if the contigs type is specified
check_var "ARG_C"
check_var "ARG_L"
## Prepare
mkdir -p $DirFasta
## Move the assemblied fasta file to the folder
if [ "$ARG_C" = "scaffolds" ] || [ "$ARG_C" = "contigs" ] ; then
for (( i=0; i<$length_fn; i++ )); do
cp $DirAssembly/${full_names[$i]}/$ARG_C.fasta $DirFasta/$ARG_C/${full_names[$i]}.fasta
done
fi
fi
### Mapping
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "map" ]; then
## Check if the reference or contigs type is specified
check_var "ARG_C"
check_var "ARG_R"
check_command "diamond"
## Prepare
mkdir -p $DirMap
## Index reference database
cd $DirFasta/$ARG_C
diamond makedb --db Reference --in $ARG_R
cd -
## Blastx for mapping DNA sequences to protein reference sequence
cd $DirFasta/$ARG_C
for (( i=0; i<$length_fn; i++ )); do
diamond blastx -d Reference.dmnd -q ${full_names[$i]}.fasta -o ${full_names[$i]}.m8 \
--outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen gaps ppos qframe qseq
# subject: reference; query: align-aimed
#1: qseqid: Query Seq-id
#2: sseqid: Subject Seq - id
#3: pident: Percentage of identical matches
#4: length: Alignment length
#5: mismatch: Number of mismatches
#6: gapopen: Number of gap openings
#7: qstart: Start of alignment in query
#8: qend: End of alignment in query
#9: sstart: Start of alignment in subject
#10: send: End of alignment in subject
#11: evalue: Expect value
#12: bitscore: Bit score
#13: qlen: Query sequence length
#14: slen: Subject sequence length
#15: gaps: Total number of gaps
#16: ppos: Percentage of positive - scoring matches
#17: qframe: Query frame (frames in blast?)
#18: qseq: Aligned part of query sequence
done
cd -
mv $DirFasta/$ARG_C/*.m8 $DirMap
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
mkdir -p $DirPre
check_var "ARG_L"
check_path "PathSortdiamond"
# extract fasta file from diamond balst style output
for (( i=0; i<$length_fn; i++ )); do
$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
done
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
mkdir -p $DirSplit
cd $DirPre
check_var "ARG_L"
check_path "PathSplitfasta"
# split fasta into different folders based on sequence names
for (( i=0; i<$length_fn; i++ )); do
$PathSplitfsata ${full_names[$i]}.fasta
done
# mv to destdir
find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
cd -
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
## Check if the genes is specified
check_var "ARG_G"
mkdir -p $DirMerge
cd $DirSplit
# merge different taxa sequences in same gene to one fasta
for (( i=0; i<$length_gn; i++ ))
do
cd ${genes[$i]}
cat * > ../${genes[$i]}.fasta
cd ..
done
# mv to destdir
mv *.fasta ../$DirMerge
cd -
fi
if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
## Check if the genes is specified
check_var "ARG_G"
check_command "java"
check_command "parallel"
check_path "PathMacse"
# current_thread=0
mkdir -p $DirAlign
mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
cd $DirMerge
# align the sequence based on codon
parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}"
cd -
fi
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