From be4682561aff30b185045033b88177efd1619271 Mon Sep 17 00:00:00 2001 From: GuilhemRoyer Date: Wed, 30 May 2018 11:46:04 +0200 Subject: [PATCH] Add files via upload --- plaScope_V1.0.sh | 263 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 263 insertions(+) create mode 100644 plaScope_V1.0.sh diff --git a/plaScope_V1.0.sh b/plaScope_V1.0.sh new file mode 100644 index 0000000..e5f6cc5 --- /dev/null +++ b/plaScope_V1.0.sh @@ -0,0 +1,263 @@ +#!/usr/bin/env bash + + +############################################################## +# Author Guilhem ROYER groyer@genoscope.cns.fr | 06/04/2018 # +############################################################## + +set -e +set -u +set -o pipefail + + +############# +# Help # +############# + +usage() +{ +cat << EOF +usage: PlaScope.sh [OPTIONS] [ARGUMENTS] + +-h, --help display this message +-t number of threads[OPTIONAL] [default : 8] +-i fastq name (assumed to be fastq_name_1.fastq.gz / fastq_name_2.fastq.gz) [MANDATORY] +--fastq_dir path to fastq directory [MANDATORY] +-o output directory [OPTIONAL] [default : current directory] +--db_dir path to centrifuge database [MANDATORY] +--db_name centrifuge database name [MANDATORY] + +Wrapper to launch PlaScope (SPAdes + Centrifuge-based plasmidic sequences classification) + + +EOF +} + + +################################ +# Just a little bit of art # +################################ + + +plascope() +{ +cat << "EOF" + +# MNXXXXXXXXXXXXNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWXXXXXXXXXXXXXXXXNMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +No'''''''''''''cOWMMWKOOOXWMMMMMMMMMMMMMMWKO0OO0000O0XMMMMNk;''''''''''''',:dXMWX00000000OO0O0NMMMN0O000000OOKNMMWX0000000000OKWMMMN0O000000000000O0NM +N: .:0W0, cNMMMMMMMMMMMMWO:. 'dXM0; ,xKNWKl. .,xNMNx,. .;kNNc .:0WMO' .'dXM +N: .:lllll; ,00' :NMMMMMMMMMMMWd. ;0d ,llllllllokNMMMO' 'dXMMX: oX: .lXk. .lKWMM +N: ,KMWWKl. .c0W0' :NMMMMMMMMMMMN: .okkkkkk; .kd .xMMMMMMMMMMMMMMd. :kkkkkkOXMMMM0' ,xkkkkkd. ;K: .okd; ,kNk. ;kkkkkkkKWMMMM +N: ,KWKl. .c0WMM0' :NMMMMMMMMMMMN: 'OOxxxxx; .kd cOkkkkkkOkOXMMMd. .xMMMMMMMMMMMM0' cWMMMMMX; ;K: ,Ox, ,xNMMk. ;xxxxxxONMMMMM +N: 'ko. .c0WMMMM0' :NMMMMMMMMMMMN: .:. .kO. 'dOXd .xMMMMMMMMMMMM0' cWMMMMMX; ;K: .:. ,xNMMMMk. .OMMMMM +N: .:. .:OWMMMMMM0' :NMMMMMMMMMMMN: 'kOxxxxx; .kWKl. :l. .xMMMMMMMMMMMM0' cWMMMMMX; ;K: ,kd,,xNMMMMMMk. ,xxxxxxONMMMMM +N: ,0O:cOWMMMMMMMM0' ,k0O0000OO0OKN: '0MMMMMMo .kMMWXOOOOOOOOOk, ':. c0OO000000O0X0' ,k0O0OOx' ;K: ,KWNNMMMMMMMMk. :O000000O00OXM +N: ,KMWWMMMMMMMMMM0' :Kc '0MMMMMMo .kMMMMMMMMMMMMMNc 'o' .dK; lK: ,KMMMMMMMMMMMk. cN +N: ,KMMMMMMMMMMMMM0, ;Kc ,0MMMMMWo .k0lcccccccccccc. 'O0c. oWXo. ,xNN: ,KMMMMMMMMMMMk. cN +N: ,KMMMMMMMMMMMMMN0kkkkkkkkkkkkkkk0WKkkk0WMMMMMMXOkkONd .;dNMWKkkkkkkkkkkkkkXMMMXOkkkkkkkkkONMMWKkkk0WMMMMMMMMMMMNOkkkkkkkkkkkkkkkKW +No',,lXMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMO;,,,',,,,,,,,,,lKWWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +MWNWNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWWWWWWWWWWWWWWWWWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +EOF +} + + +#print on stderr +echoerr() { printf "%s\n" "$*" >&2; } + + +######################## +### Contig sorting ## +######################## + + +contig_sorting() +{ + +local plascopeextendres="$1" + +local contigcov=${CONTIGCOV} +local contiglength=${CONTIGLENGTH} +local hitlength=${HITLENGTH} + +awk -F'\t' -v contigcov=${contigcov} -v contiglength=${contiglength} -v hitlength=${hitlength} ' +BEGIN { +TPLASCOPERES[0]="unclassified" +TPLASCOPERES[1]="unclassified" +TPLASCOPERES[2]="chromosome" +TPLASCOPERES[3]="plasmid" +OFS="\t" + +#skip first line +getline +} + +{clab=$1; split(clab,T,"_") ; ccov=T[6]; + +if ( $7>=contiglength && $6>=hitlength && ccov>contigcov ) print $1,TPLASCOPERES[$3] + +else print $1,TPLASCOPERES[0] + +}' $plascopeextendres + +} + + + +######################################### +###### Awk fasta extraction ####### +######################################### + +contig_extraction() +{ + +local contigfile="$1" +local contigsortingfile="$2" +local contigfileprefix="$3" + +awk -F'\t' -v contigfileprefix=${contigfileprefix} ' +NR==FNR{Tcontig[">"$1]=$2;next} + +/^>/ { +if ($1 in Tcontig) output=contigfileprefix"_"Tcontig[$1]".fasta" +else +{ +print "Warning:", $1, "not classified." > "/dev/stderr" +output="" +} + +} + +output { print > output }' $contigsortingfile $contigfile + +} + + +#################################### +#### Get argument with getopts ##### +#################################### + +while getopts ":i:o:d:t:-:h" optchar; do + case "${optchar}" in + -) + case "${OPTARG}" in + help) + usage + exit + ;; + db_dir) + CENTRI_DIR="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) + ;; + db_name) + DB_NAME="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) + ;; + fastq_dir) + FQ_DIR="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 )) + ;; + esac;; + h) + usage + exit + ;; + i) + INPUT=${OPTARG} + ;; + t) + THREADS=${OPTARG} + ;; + o) + O_DIR=${OPTARG} + ;; + ?) + usage + exit + ;; + esac +done + + + + +if [[ -z "${INPUT:-}" ]] || [[ -z "${CENTRI_DIR:-}" ]] || [[ -z "${DB_NAME:-}" ]] +then + usage + exit +fi + +# Set default values of optional parameters +if [[ -z "${THREADS:-}" ]] +then + # default value: 8 + THREADS=8 +fi + +if [[ -z "${FQ_DIR:-}" ]] +then + # default value: current directory + FQ_DIR="." +fi + +if [[ -z "${O_DIR:-}" ]] +then + # default value: current directory + O_DIR="." +fi +#Remove trailing slash of paths if exist +FASTQ_DIR=${FQ_DIR%/} +DB_DIR=${CENTRI_DIR%/} +OUTPUT=${O_DIR%/} + +######################## +#### Run functions ##### +######################## + + +if [[ -d "${OUTPUT}/${INPUT}_PlaScope/PlaScope_predictions" ]] +then + echoerr "${OUTPUT}/${INPUT}_PlaScope/PlaScope_predictions already exists" + exit 1 +else +mkdir -p ${OUTPUT}/${INPUT}_PlaScope/PlaScope_predictions +fi + +if [[ -d "${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results" ]] +then + echoerr "${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results already exists" + exit 1 +else +mkdir -p ${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results +fi + + +#plascope variables for contig evaluation +readonly CONTIGCOV=2 +readonly CONTIGLENGTH=500 +readonly HITLENGTH=100 + + +plascope + +#Step 1/3 + +echo "Step 1/3: Running assembly with SPAdes 3.10.1" + +spades.py --careful -t ${THREADS} -1 ${FASTQ_DIR}/${INPUT}_1.fastq.gz -2 ${FASTQ_DIR}/${INPUT}_2.fastq.gz -o ${OUTPUT}/${INPUT}_PlaScope/SPAdes + +#Step 2/3 + +echo "Step 2/3: Contigs classification with Centrigue and custom database" + +export CENTRIFUGE_INDEXES=${DB_DIR} +centrifuge -f --threads ${THREADS} -x ${DB_NAME} -U ${OUTPUT}/${INPUT}_PlaScope/SPAdes/contigs.fasta -k 1 --report-file ${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results/${INPUT}_summary -S ${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results/${INPUT}_extendedresult + +#Step 3/3 + +echo "Step 3/3: Extraction of plasmid, chromosome and unclassified predictions" + +contig_sorting ${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results/${INPUT}_extendedresult > ${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results/${INPUT}_list + +contig_extraction ${OUTPUT}/${INPUT}_PlaScope/SPAdes/contigs.fasta ${OUTPUT}/${INPUT}_PlaScope/Centrifuge_results/${INPUT}_list ${OUTPUT}/${INPUT}_PlaScope/PlaScope_predictions/${INPUT} + +echo "If you use PlaScope please cite : ..." + +exit 0