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plaScope_V1.0.sh

@@ -0,0 +1,263 @@
+#!/usr/bin/env bash
+
+
+##############################################################
+# Author Guilhem ROYER [email protected] | 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