tag >> 0.2.0

README.md

@@ -185,7 +185,7 @@ iedb=~/Variants2Neoantigen/data/iedb/iedb.fasta                # iedb database u
 ##PATH_HLA=~/wangshx/projects/data/                         # directory path to patient specific HLA alleles file
 
 ####### <<<<<< Location of Softwares, python environment and input arguments
-py_env=pipeline                                                # python environment, which can run pvacseq 
+py_env=pipeline                                                # python environment, which can run pvacseq (Python 3.5) 
 py2_env=py2     # python2.7 
 
 maf2vcf=~/vcf2maf/maf2vcf.pl      # path of maf2vcf.pl script

add_path.sh

@@ -1,12 +1,18 @@
 #!/bin/bash
-# add runNEO path to ~/.bashrc
+# add Variants2neoantigen path to ~/.bashrc
 
+echo "Add permission for scripts..."
+chmod u+x *.sh runNEO
+
+echo "Add path for Variants2neoantigen tool..."
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
-echo "# add path for runNEO tool" >> ~/.bashrc
+echo "# add path for Variants2neoantigen tool" >> ~/.bashrc
 echo 'export' PATH=\""$DIR:\$PATH"\" >> ~/.bashrc
 source ~/.bashrc
 
-echo "Add runNEO path to your ~/.bashrc successfully!"
+echo "Add Variants2neoantigen path to your ~/.bashrc successfully!"
 echo "==> Please open a new terminal or run source ~/.bashrc handly before using it."
+
+
 exit
 

configureArgs

@@ -1,15 +1,12 @@
 # This file is used to configure default parameters of neoantigens computation
-# If you do not know what it means, DO NOT change it!!!
-# If you want help, free to send email to <wangshx@shanghaitech.edu.cn> 
+# Please change the content following the provided format
+# If you want help, free to send email to <wangshx@shanghaitech.edu.cn> or open an issue at <https://github.com/ShixiangWang/Variants2Neoantigen/issues>
 
 ####### <<<<<< Location of Files
-##maffiles=$(pwd)/*.maf                       # location of maf file
-##OUTPUT=$(pwd)/neoantigen_results
 CACHE_VEP=~/.vep/                                           # directory path of ensembl vep cache
 PATH_FASTA=~/.vep/homo_sapiens/92_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa           
                                                             # path of reference fasta file
-iedb=~/Variants2Neoantigen/data/iedb/iedb.fasta                # iedb database used for blastp
-##PATH_HLA=~/wangshx/projects/data/                         # directory path to patient specific HLA alleles file
+iedb=~/Variants2Neoantigen/data/iedb/iedb.fasta             # iedb database used for blastp
 
 ####### <<<<<< Location of Softwares, python environment and input arguments
 py_env=pipeline                                                # python environment, which can run pvacseq 

runNEO_prepare

@@ -0,0 +1,87 @@
+#! /usr/bin/env bash
+# Generate configure file before computation.
+# input file and HLA must provide
+
+####################################
+### Parsing option using getopts ###
+####################################
+
+# i or --input: input maf (or vcf -> enhancement)path
+# o or --output: output directory path
+# --HLA: HLA file path
+# --mode: maf or vcf ? -> enhancement
+# --seq: workflow? -> enhancement
+optspec=":hi:o:-:"
+while getopts "$optspec" optchar; do
+    case "${optchar}" in
+        -)
+            case "${OPTARG}" in
+                loglevel)
+                    val="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
+                    echo "Parsing option: '--${OPTARG}', value: '${val}'" >&2;
+                    ;;
+                #loglevel=*)
+                #    val=${OPTARG#*=}
+                #    opt=${OPTARG%=$val}
+                #    echo "Parsing option: '--${opt}', value: '${val}'" >&2
+                #    ;;
+                HLA)
+                    val="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
+                    echo "The HLA path is $val";
+					PATH_HLA=$val
+                    ;;				
+                *)
+                    if [ "$OPTERR" = 1 ] && [ "${optspec:0:1}" != ":" ]; then
+                        echo "Unknown option --${OPTARG}" >&2
+                    fi
+                    ;;
+            esac;;
+        h)
+            echo "usage: $0 [-i <input_file>] [-o <output_dir>] [--HLA <HLA_file>]" >&2
+            exit 2
+            ;;
+        i)
+            echo "The input file path is $OPTARG"
+			maffiles=$OPTARG
+            ;;
+		o)
+            echo "The output directory path is $OPTARG"
+			OUTPUT=$OPTARG
+            ;;	
+        *)
+            if [ "$OPTERR" != 1 ] || [ "${optspec:0:1}" = ":" ]; then
+                echo "Non-option argument: '-${OPTARG}'" >&2
+		exit 2
+            fi
+            ;;
+    esac
+done
+
+# if variable name is not set, show help info
+if [ ! -n "$maffiles" ]; then
+	runNEO_prepare -h
+	exit
+fi
+
+if [ ! -n "$OUTPUT" ]; then
+	OUTPUT=`pwd`
+fi
+
+if [ ! -n "$PATH_HLA" ]; then
+	runNEO_prepare -h
+	exit
+fi
+
+# generate a args file
+echo "Configuration file generating..."
+ShellDIR=$(cd `dirname $0`; pwd)
+
+source $ShellDIR/configureArgs
+cat $ShellDIR/configureArgs | grep -v "^##" | grep -v "ShellDIR" > $(pwd)/inputArgs.txt
+echo "maffiles=$maffiles" >> $(pwd)/inputArgs.txt
+echo "OUTPUT=$OUTPUT" >> $(pwd)/inputArgs.txt
+echo "PATH_HLA=$PATH_HLA" >>  $(pwd)/inputArgs.txt
+echo "ShellDIR=$ShellDIR" >> $(pwd)/inputArgs.txt
+
+echo "Configure file inputArgs.txt has been successfully generated in current directory."
+echo "Please modify nessary arguments and run runNEO_run to start the pipeline."

runNEO_run

@@ -0,0 +1,38 @@
+#! /usr/bin/env bash
+# Run neoantigen computation, which will use configure file in current directory.
+
+
+# load arguments from configure file
+source $(pwd)/inputArgs.txt
+
+source activate $py_env
+# check if software commands exist
+type blastp >/dev/null 2>&1 || { echo >&2 "blastp is need but it's not installed in $py_env environment .  Aborting."; exit 1; }
+type pvacseq >/dev/null 2>&1 || { echo >&2 "pvacseq is need but it's not installed in $py_env environment.  Aborting."; exit 1; }
+type samtools >/dev/null 2>&1 || { echo >&2 "samtools is need but it's not installed in $py_env environment.  Aborting."; exit 1; }
+
+echo ----------------------
+echo --- Pipeline Begin ---
+echo ----------------------
+
+#step1: transform maf files to vcf files
+$ShellDIR/step1-transformMaf2VCF.sh
+
+# step2: run neoantigen computation, choose only one way as follows to run, other line should be commented
+
+# serial way
+#$ShellDIR/step2-NEOcomputation_serial.sh 
+
+# parallel way
+$ShellDIR/step2-NEOcomputation_parallel.sh 
+
+# step3: summary neoantigen results
+# $ShellDIR/step3-summaryNeoantigens.sh
+
+# step3: calculate neoantigen quality
+$ShellDIR/step3-neoantigenQcomputation.sh
+
+echo --------------------
+echo --- Pipeline End ---
+echo --------------------
+