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|
#!/bin/bash
#*****************************************************************************
# VCF_Creator: mapping and VCF creation feature in DiscoSnp++
# Copyright (C) 2015 INRIA
# Author: C.Riou
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#*****************************************************************************
# First check that python3 is installed and has version 3 or more:
if ! hash python3; then
echo "python3 is not installed"
exit 1
fi
ver=$(python3 -V 2>&1 | sed 's/.* \([0-9]\).\([0-9]\).*/\1\2/')
if [ "$ver" -lt "30" ]; then
echo "This script requires python3 3.0 or greater"
exit 1
fi
# Get the local directory path
DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
# Option initialisations and defaults
remove=0
PATH_VCF_creator=""
samfile=""
vcffile=""
genome=""
PATH_BWA=""
discoSNPs=""
bwa_threads=""
k=19
n=""
s=0
igv=0
map_with_extensions=0
function help {
echo " ##############################"
echo " Run VCF_creator pipeline "
echo " ##############################"
echo "Usage : ./run_VCF_creator.sh OPT"
echo -e "##MODE 1: WITHOUT REFERENCE GENOME. Create a vcf file without alignment:"
echo -e "\t\t./run_VCF_creator.sh -p <disco_file> -o <output> [-w]"
echo -e "##MODE 2: ALIGNING AGAINST A REFERENCE GENOME:"
echo -e "\t\t./run_VCF_creator.sh -G <ref> -p <disco_file> -o <output> [-B <path_bwa>] [-w] [-e]"
echo -e "##MODE 3: USING A HOME MADE ALIGNMENT. Samfile from bwa already exists: "
echo -e "\t\t./run_VCF_creator.sh -f <sam_file> -o <output> [-w]"
echo
echo -e "\t-h: print this message"
echo -e "\t-p: discosnp++ output file (foo_coherent.fa)"
echo -e "\t\t Mandatory unless MODE 3"
echo -e "\t-o: output <file> (VCF format)"
echo -e "\t\t Mandatory"
#echo -e "\t-c : path where VCF_creator is"
echo -e "\t-G: reference genome (Fasta format)"
echo -e "\t\t Optional unless MODE 2: you want the mapping positions of the predicted variants in the VCF file and you do not provide a third-party sam file. E.G.: -B and -G options must be used together"
echo -e "\t-B: bwa path. i.e. /home/me/my_programs/bwa-0.7.12/ (note that bwa must be pre-compiled)"
echo -e "\t\t Optional unless MODE 2 if bwa is not in the binary path. E.G.: -B and -G options must be used together"
echo -e "\t-I : Creation of output specific to IGV (Integrative Genomics Viewer)"
echo -e "\t\t Optional"
echo -e "\t-f: <file>.sam: skip the alignment phases to create the vcf file"
echo -e "\t\t Optional unless MODE 3: you want the mapping positions of the predicted variants in the VCF file without remapping on a reference genome. -f option must be used together with -n"
echo -e "\t-k: bwa option: seed size"
#echo -e "\t\t Optional, default 0"
#echo -e "\t-l: bwa option: length of the seed for alignment"
#echo -e "\t\t Optional, default 10"
#echo -e "\t-n: bwa option: maximal bwa mapping distance"
echo -e "\t\t Optional in MODE 1 AND 2, default 3 - warning, bwa mapping running time highly depends on this parameter."
echo -e "\t\t Mandatory in MODE 3. "
echo -e "\t-t: bwa option: Number of threads (default=unlimited) "
echo -e "\t-w: remove index files ( <.amb>, <.ann>, <.bwt>, <.pac>, <.sa> )"
echo -e "\t\t Optional"
echo -e "\t-e: Map SNP predictions with their extensions on reference genome"
}
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
while getopts "hB:c:G:p:wk:Ief:o:t:" opt; do
case $opt in
t)
bwa_threads="-t $OPTARG"
;;
w)
remove=1
;;
h)
help
exit 1
;;
B)
echo -e "\t##BWA directory: $OPTARG" >&2
PATH_BWA=$OPTARG
;;
# c)
# echo -e "\t##VCF_creator directory: $OPTARG" >&2
# PATH_VCF_creator=$OPTARG
# ;;
G)
echo -e "\t##use genome : $OPTARG" >&2
genome=$OPTARG
;;
p)
echo -e "\t##use disco SNPS : $OPTARG" >&2
discoSNPs=$OPTARG
;;
# s)
# echo -e "\t##use distance with the seed : $OPTARG" >&2
# s=$OPTARG
# ;;
# n)
# echo -e "\t##use number of mismatches : $OPTARG" >&2
# n=$OPTARG
# ;;
k)
echo -e "\t##use bwa seed length : $OPTARG" >&2
k=$OPTARG
;;
f)
echo -e "\t##use directly samfile : $OPTARG" >&2
samfile=$OPTARG
;;
I)
echo -e "\t##Will create a vcf file for IGV : Sorting VCF by mapping positions and removing unmapped variants"
igv=1
;;
e)
echo -e "\t##Predictions will be mapped with their extensions on reference genome"
map_with_extensions=1
;;
o)
echo -e "\t##output : $OPTARG" >&2
vcffile=$OPTARG
;;
\?)
echo -e "##Invalid option: -$OPTARG" >&2
exit 1
;;
:)
echo "##Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
###Tests
if [ -z "$vcffile" ];then
if [ ! -z "$samfile" ];then
echo -e "..To skip the alignment phase ..."
echo -e "\t./run_VCF_creator.sh -f <sam_file> -n <mismatch_number> -o <output> [-k <seed_size>] [-s <bwa_errors_in_seed>] [-w]"
exit 1
else
help
exit 1
fi
fi
# if [ -z "$PATH_VCF_creator" ];then
# PATH_VCF_creator=$DIR""
# fi
PATH_VCF_creator=$DIR
if [ ! -e $PATH_VCF_creator/VCF_creator.py ]; then
echo "...Unable to find VCF_creator..."
exit 1
fi
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
####Use the pipeline of aligement
if [ -z "$samfile" ];then
if [ ! -z "$vcffile" ] && [ -z "$genome" ] && [ -z "$discoSNPs" ]; then
help
exit 1
fi
#Ghost mode
if [ -z "$genome" ]; then
# if [[ "$discoSNPs" =~ sam ]]; then
# echo "$discoSNPs"
# echo "!!! Disco file can't be a sam file !!!"
# exit 1
# fi
echo -e "...Ghost mode..."
echo -e "...Creation of a vcf without alignment..."
if [ -z "$discoSNPs" ] && [ -z "$vcffile" ];then
echo -e "...To create a vcf without alignment ..."
echo -e "...You must provide an output <file>.vcf : option -o..."
echo -e "...And the file disco : option -p..."
exit 1
else
echo -e " run python3 $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile"
python3 $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile #-n $n
if [ $? -ne 0 ]
then
echo "there was a problem with the VCF creation (command was \"python3 $PATH_VCF_creator/VCF_creator.py -s $discoSNPs -o $vcffile\""
exit 1
fi
echo -e "... Creation of the vcf file : done ...==> $vcffile"
echo -e " Transforming the created zero-based vcf onto a one-based vcf file"
cmd="python3 $PATH_VCF_creator/zero2one.py -i $vcffile"
echo $cmd
$cmd
exit
fi
fi
if [ -z "$PATH_BWA" ] ;then
IS_BWA=$(command -v bwa)
if [ -z "$IS_BWA" ];then
echo -e "... BWA not found... add bwa to \$PATH or give directly the path (-B)"
exit 1
else
PATH_BWA=$(dirname $IS_BWA)
fi
fi
if [ -z "$vcffile" ] ; then
echo -e "...You must provide an output <file> : option -o (for help -h)..."
help
exit 1
fi
if [ -z "$genome" ]; then
echo -e "...You must provide a genome of reference : option -G (for help -h)..."
help
exit 1
fi
if [ -z "$discoSNPs" ];then
echo "... Error : file disco is missing : option -p (for help -h)..."
help
exit 1
else
if [ ! -e $PATH_VCF_creator/remove_extensions_disco_file.py ];then
echo "...Unable to find remove_extensions_disco_file.py..."
exit 1
else
discoSNPsbis=$(basename $discoSNPs .fa)"bis.fasta"
if [ $map_with_extensions -eq 1 ];then
python3 $PATH_VCF_creator/keep_extensions_disco_file.py $discoSNPs $discoSNPsbis
else
python3 $PATH_VCF_creator/remove_extensions_disco_file.py $discoSNPs $discoSNPsbis
fi
if [ -z "$discoSNPsbis" ];then
echo "...Error with the script remove_extensions_disco_file.py..."
exit 1
fi
fi
fi
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
#BWA files
#Pierre: user gave a file name we must respect its choice.
# vcf=$(basename $vcffile .vcf)"_"$(basename $discoSNPs .fa)"_n"$n"_l"$l"_s"$s".vcf"
samfile=$(basename $discoSNPs .fa)"BWA_MEM".sam
indexamb=$genome".amb"
indexann=$genome".ann"
indexbwt=$genome".bwt"
indexpac=$genome".pac"
indexsa=$genome".sa"
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
##Indexation of reference genome
if [ -e $indexamb ] && [ -e $indexann ] && [ -e $indexbwt ] && [ -e $indexpac ] && [ -e $indexsa ]; then
echo -e "...Indexation : Using the existing index..."
else
echo "INDEXATION: $PATH_BWA/bwa index $genome"
$PATH_BWA/bwa index $genome
if [ $? -ne 0 ]
then
echo "there was a problem with BWA (command was \"$PATH_BWA/bwa index $genome\""
exit 1
fi
fi
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
##Alignment discosnps on the reference genome
echo "ALIGNMENT: $PATH_BWA/bwa mem -h 80 -k $k $genome $discoSNPsbis $bwa_threads > $samfile"
$PATH_BWA/bwa mem -h 80 -k $k $genome $discoSNPsbis $bwa_threads > $samfile
if [ $? -ne 0 ]
then
echo "there was a problem with BWA (command was \"$PATH_BWA/bwa mem -h 80 -k $k $genome $discoSNPsbis $bwa_threads > $samfile\""
exit 1
fi
#---------------------------------------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------------------------------------
else
####Skip alignment phase to create a vcf file
##Test to execute VCF_creator
echo -e "...Skipping alignment phase..."
if [ -z "$vcffile" ] || [[ "$vcffile" =~ *.vcf ]]; then
echo -e "...You must provide an output <file>..."
exit 1
fi
fi
echo -e "python3 $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile"
python3 $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile
if [ $? -ne 0 ]
then
echo "there was a problem with the VCF creation (command was \"python3 $PATH_VCF_creator/VCF_creator.py -s $samfile -o $vcffile \""
exit 1
fi
echo -e "... Creation of the vcf file: done ...==> $vcffile "
if [ $igv -eq 1 ] ; then
$DIR/create_IGV_compatible_VCF.sh $vcffile
nameVCFIGV=$( basename $vcffile .vcf )
python3 $PATH_VCF_creator/filterOnBestDP_multiple_variant_at_same_pos.py $nameVCFIGV\_for_IGV.vcf > tmp.vcf
if [ $? -ne 0 ]
then
echo "there was a problem with the IGV VCF creation (command was \"python3 $PATH_VCF_creator/filterOnBestDP_multiple_variant_at_same_pos.py $nameVCFIGV\_for_IGV.vcf > tmp.vcf\""
exit 1
fi
echo -e "... Creation of the vcf file: done ...==> $vcffile"
cat tmp.vcf > $nameVCFIGV\_for_IGV.vcf
echo -e " Transforming the created zero-based vcf (and for IGV vcf) onto one-based vcf files"
cmd="python3 $PATH_VCF_creator/zero2one.py -i $vcffile"
echo $cmd
$cmd
cmd="python3 $PATH_VCF_creator/zero2one.py -i ${nameVCFIGV}_for_IGV.vcf"
echo $cmd
$cmd
fi
if [ $remove -eq 1 ];then
rm -f $indexamb $indexann $indexbwt $indexpac $indexsa $saifile $discoSNPsbis tmp.vcf
else
rm -f tmp.vcf $discoSNPsbis
fi
|
