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runRufus.sh
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runRufus.sh
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#!/bin/bash
set -e
# This is a rather minimal example Argbash potential
# Example taken from http://argbash.readthedocs.io/en/stable/example.html
# ARG_OPTIONAL_SINGLE([subject],[s],[generator file containing the subject of interest])
# ARG_OPTIONAL_SINGLE([ref],[r],[file path to the desired reference file])
# ARG_OPTIONAL_SINGLE([threads],[t],[number of threads to use])
# ARG_OPTIONAL_SINGLE([kmersize],[k],[size of Khmer to use])
# ARG_OPTIONAL_SINGLE([min],[m],[overwrites the minimum k-mer count to call variant])
# ARG_POSITIONAL_INF([controls],[generator files containing the control subjects],[0])
# ARG_HELP([The general script's help msg])
# ARGBASH_GO()
# needed because of Argbash --> m4_ignore([
### START OF CODE GENERATED BY Argbash v2.5.1 one line above ###
# Argbash is a bash code generator used to get arguments parsing right.
# Argbash is FREE SOFTWARE, see https://argbash.io for more info
# Generated online by https://argbash.io/generate
start_time=$(date +"%s")
echo "RUFUS version C.0.1"
echo -e "RUFUS command was: $0 $@"
date
MaxHashDepth=1200; #need to make this a passed option
RDIR=/opt/RUFUS
BOUND_DATA_DIR=/mnt
cd $BOUND_DATA_DIR
die()
{
local _ret=$2
test -n "$_ret" || _ret=1
test "$_PRINT_HELP" = yes && print_help >&2
echo "$1" >&2
exit ${_ret}
}
begins_with_short_option()
{
local first_option all_short_options
all_short_options='srtkmh'
first_option="${1:0:1}"
test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
}
# THE DEFAULTS INITIALIZATION - POSITIONALS
_positionals=()
_arg_exclude=()
# THE DEFAULTS INITIALIZATION - OPTIONALS
_arg_controls=()
_arg_subject=
_arg_ref=
_arg_threads=3
_arg_kmersize=25
_arg_min=5
_arg_refhash=
_arg_saliva="FALSE"
_arg_exome="FALSE"
_MaxAlleleSize="1000"
_arg_mosaic="FALSE"
_assemblySpeed="full"
_parallel_jelly="no"
_pairedEnd="true"
_arg_region=
_arg_filterK=1
_arg_ParLowK=2
_filterMinQ=15
_arg_stop="nope"
_arg_dev_reporting="FALSE"
_arg_dev_file_output="FALSE"
print_help ()
{
printf "%s\n" "The general script's help msg"
printf 'Usage: %s [-s|--subject <arg>] [-r|--ref <arg>] [-t|--threads <arg>] [-k|--kmersize <arg>] [-m|--min <arg>] [-h|--help] [<controls-1>] ... [<controls-n>] ...\n' "$0"
printf "\t%s\n" "-s,--subject: bam/cram/fastq(or pair of fastq files)/generator file containing the subject of interest (no default, only one subject per run for now)"
printf "\t%s\n" "-c, --controls: bam/cram/fastq(or pair of fastq files)/generator file for the sequence data of the control sample (can be used multipe times)"
printf "\t%s\n" "-e,--exclude: Jhash file of kmers to exclude from mutation list, k must be (no default, can be used multiple times)"
printf "\t%s\n" "-se, --single_end_reads: subject bam file is single end reads, not paired (default is to assume paired end data)"
printf "\t%s\n" "-r,--ref: file path to the desired reference file (no default)"
printf "\t%s\n" "-cr,--cramref: file path to the desired reference file to decompress input cram files (no default)"
printf "\t%s\n" "-t,--threads: number of threads to use (no default) (min 3)"
printf "\t%s\n" "-k,--kersize: size of k-mer to use (no default)"
printf "\t%s\n" "-m,--min: overwrites the minimum k-mer count to call variant (no default)"
printf "\t%s\n" "-i, --saliva: flag to indicate that the subject sample is a buccal swab and likely contains a significant fraction of contaminant DNA"
printf "\t%s\n" "-mx, --MaxAllele: Max size for insert/deletion events to put the entire alt sequence in. (default 1000)"
printf "\t%s\n" "-L, --Report_Low_Freq: Reprot Mosaic/Low Frequency/Somatic variants (default FALSE)"
printf "\t%s\n" "-CLEAN: Does not do a rufus run but cleans up intermediate files created by RUFUS"
printf "\t%s\n" "-o, --devOutput: Prints very verbose run information to stdout"
printf "\t%s\n" "-h,--help: Print help"
printf "\t%s\n" "-d: Print dev help"
}
print_devhelp ()
{
printf "%s\n" "The general script's help msg"
printf 'Usage: %s [-s|--subject <arg>] [-r|--ref <arg>] [-t|--threads <arg>] [-k|--kmersize <arg>] [-m|--min <arg>] [-h|--help] [<controls-1>] ... [<control\
s-n>] ...\n' "$0"
printf "\t%s\n" "-s,--subject: bam/cram/fastq(or pair of fastq files)/generator file containing the subject of interest (no default, only one subject per run for now)"
printf "\t%s\n" "-c, --controls: bam/cram/fastq(or pair of fastq files)/generator file for the sequence data of the control sample (can be used multiple times)"
printf "\t%s\n" "-e,--exclude: Jhash file of kmers to exclude from mutation list, k must be (no default, can be used multiple times)"
printf "\t%s\n" "-se, --single_end_reads: subject bam file is single end reads, not paired (default is to assume paired end data)"
printf "\t%s\n" "-r,--ref: file path to the desired reference file (no default)"
printf "\t%s\n" "-cr,--cramref: file path to the desired reference file to decompress input cram files (no default)"
printf "\t%s\n" "-t,--threads: number of threads to use (no default) (min 3)"
printf "\t%s\n" "-k,--kmersize: size of k-mer to use (no default)"
printf "\t%s\n" "-m,--min: overwrites the minimum k-mer count to call variant (no default)"
printf "\t%s\n" "-i, --saliva: flag to indicate that the subject sample is a buccal swab and likely contains a significant fraction of contaminant DNA"
printf "\t%s\n" "-mx, --MaxAllele: Max size for insert/deletion events to put the entire alt sequence in. (default 1000)"
printf "\t%s\n" "-L, --Report_Low_Freq: Report Mosaic/Low Frequency/Somatic variants (default FALSE)"
printf "\t%s\n" "-z, --Dev output: Keep all intermediate files produced by RUFUS (default FALSE)"
printf "\t%s\n" "-CLEAN: Does not do a rufus run but cleans up intermediate files created by RUFUS"
printf "\t%s\n" "################################################################################################"
printf "\t%s\n" "Extra options, mosstly experimental or algorithm parameters that you normaly dont need to adjust"
printf "\t%s\n" "################################################################################################"
printf "\t%s\n" "-f,--refhash: Jhash file containing reference hashList (no default)"
printf "\t%s\n" "-mx, --MaxAllele: Max size for insert/deletion events to put the entire alt sequence in. (default 1000)"
printf "\t%s\n" "-ex, --exome: flag to set if your input data is exome sequencing. Distribution model is not used, -m = 20, saliva fix is set, max kmer depth set to 1 million (EXPERIMENTAL values used here have not been exhaustivly tested)"
printf "\t%s\n" "-q1,--fastq1: If starting from fastq files, a list of the mate1 fastq files to improve RUFUS.filter"
printf "\t%s\n" "-q2,--fastq2: If starting from fastq files, a list of the mate2 fastq files to improve RUFUS.filter"
printf "\t%s\n" "-vs, --Very_Short_Assembly: use very short assembly methods, recommended when you are expecting over 10,000 variants "
printf "\t%s\n" "-pj, --Parallelize_Jelly: parallelize jellyfish step, only use if you have more than 96G of ram"
printf "\t%s\n" "-R, --Region: Run RUFUS only on a samtools style region"
printf "\t%s\n" "-fk, --filterK: kmer threshold for number of kmers required to keep a read during filtering (default = 1)"
printf "\t%s\n" "-fq, --filterMinQ: Minimum base quality for filter step, any kmer with any bases lower than this quality will be ignored (default = 15)"
printf "\t%s\n" "-pl, --ParLowK: Lowest kmer count to be kept when counting parent jellyfish tables (default = 2, using 1 will SIGNIFICANTLY increase run time and is not advised)"
printf "\t%s\n" "-StJ: Stop run after jellyfish steps" #TODO: dont require reference and other non needed options if this is set
printf "\t%s\n" "-StH: Stop run after hash compare steps" #TODO: dont require reference and other non needed options if this is set
printf "\t%s\n" "-StF: Stop run after filter steps"
printf "\t\t%s\n" "This can be useful when you know you have low level contamination and want to remove kmers up to a certain count"
printf "\t%s\n" "-h,--help: HELP!!!!!!!!!!!!!!!"
printf "\t%s\n" "-d,--devhelp: HELP!!! for developers"
}
re='^[0-9]+$';
parse_commandline ()
{
while test $# -gt 0
do
_key="$1"
case "$_key" in
-s|--subject)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
FileName=$(basename "$2")
Extension="${FileName##*.}"
genName=$FileName
if [[ $Extension == 'fastq' ]] || [[ $Extension == 'fq' ]] || [[ $Extension == 'gz' ]] ; then
echo "" > "$FileName".generator
_arg_subject=("$FileName".generator)
fi
while [[ $2 != -* ]]; do
FileName=$(basename "$2")
Extension="${FileName##*.}"
if [ $Extension = "fastq" ] || [ $Extension = "fq" ] || [ $Extension = "gz" ]
then
echo "Warning: fastq files not currently recommended"
if [[ $Extension == 'gz' ]]
then
echo "perl $RDIR/scripts/FastqToSam.pl <(zcat $2)" >> "$genName".generator
else
echo "perl $RDIR/scripts/FastqToSam.pl <(cat $2)" >> "$genName".generator
fi
else
_arg_subject=("$2")
fi
shift
done
;;
-r|--ref)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_ref="$2"
shift
;;
-cr|--cramref)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_cramref="$2"
shift
;;
-q1|--fastq1)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_fastqA="$2"
shift
;;
-q2|--fastq2)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_fastqB="$2"
shift
;;
-t|--threads)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_threads="$2"
if ! [[ $_arg_threads =~ $re ]] ; then
echo "Threads must be a number "
exit 100
fi
shift
;;
-f|--refhash)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_refhash="$2"
shift
;;
-k|--kmersize)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_kmersize="$2"
shift
;;
-c|--controls)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
#echo "checking parent count $#"
FileName=$(basename "$2")
Extension="${FileName##*.}"
genName=$FileName
if [[ $Extension == 'fastq' ]] || [[ $Extension == 'fq' ]] || [[ $Extension == 'gz' ]] ; then
echo "" > "$FileName".generator
_arg_controls+=("$FileName".generator)
fi
while [[ $2 != -* ]]; do
FileName=$(basename "$2")
Extension="${FileName##*.}"
if [ $Extension = "fastq" ] || [ $Extension = "fq" ] || [ $Extension = "gz" ]
then
echo "fastq file identified"
if [[ $Extension == 'gz' ]]
then
echo "perl $RDIR/scripts/FastqToSam.pl <(zcat $2)" >> "$genName".generator
else
echo "perl $RDIR/scripts/FastqToSam.pl <(cat $2)" >> "$genName".generator
fi
else
_arg_controls+=("$2")
fi
shift
done
;;
-e|--exclude)
test $# -lt 2 && die "Missing value for the optional argument '$key'." 1
_arg_exclude+=("$2")
shift
;;
-m|--min)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_min="$2"
if ! [[ $_arg_min =~ $re ]] ; then
echo "arg -m must be a number "
exit 100
fi
shift
;;
-fk|--filterK)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_filterK=$2
if ! [[ $_arg_filterK =~ $re ]] ; then
echo "arg -fk or --filterK must be a number "
exit 100
fi
shift
;;
-fq|--filterMinQ)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_filterMinQ=$2
if ! [[ $_filterMinQ =~ $re ]] ; then
echo "arg -fq or --filterMinQ must be a number "
exit 100
fi
shift
;;
-pl|--ParLowK)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_ParLowK=$2
if ! [[ $_arg_ParLowK =~ $re ]] ; then
echo "arg -pl or --ParLowK must be a number "
exit 100
fi
shift
;;
-R|--region)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_region="$2"
if [[ -z $_arg_region ]] ; then
echo "arg region must not be empyty"
exit 100
fi
shift
;;
-i|--saliva)
_arg_saliva="TRUE"
echo "INFO: Saliva subject sample provided"
;;
-vs|--Very_Short_Assembly|--vs)
_assemblySpeed="veryfast"
echo "INFO: Very fast assembly being used"
;;
-se|--single_end_reads|--se)
_pairedEnd="false"
echo "INFO: Sample Bam file is single end data"
;;
-pj|--Parallelize_Jelly|--pj)
_parallel_jelly="yes"
echo "INFO: Paralellizing jellyfish, assuming 3 samples"
;;
-ex|--exome)
_arg_exome="TRUE"
echo "INFO: Exome run"
;;
-A|--MaxAllele)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_MaxAlleleSize="$2"
if ! [[ $_MaxAlleleSize =~ $re ]] ; then
echo "MaxAlleleSize must be a number "
exit 100
fi
echo "INFO: MaxAlleleSize set to $_MaxAlleleSize"
shift
;;
-L|--Report_Low_Freq)
_arg_mosaic="TRUE"
echo "INFO: Reporting mosaic/low frequency variants"
;;
-h|--help)
print_help
exit 0
;;
-h*)
print_help
exit 0
;;
-d|--devhelp)
print_devhelp
exit 0
;;
-StJ)
_arg_stop="jelly";
echo "Stopping run after jellyfish steps";
;;
-StH)
_arg_stop="hash";
echo "Stopping run after hash compare steps";
;;
-StF)
_arg_stop="filter"
echo "Stopping run after filter steps";
;;
-o)
_arg_dev_reporting="TRUE"
echo "Verbose developer reporting to stdout"
;;
-z)
_arg_dev_file_output="TRUE"
echo "Retain all intermediate files created by RUFUS run"
;;
-local)
# TODO: get rid of this before publication
RDIR=/home/ubuntu/RUFUS
;;
-CLEAN)
echo "Cleaning up intermediate files";
rm *generator.Jhash *generator.Jhash.histo *generator.Jhash.histo.7.7.dist *generator.Jhash.histo.7.7.out *generator.Jhash.histo.7.7.prob *generator.k25_c4.HashList *generator.Mutations.Mate1.fastq *generator.Mutations.Mate2.fastq *.generator.temp *.generator.temp.mate1.fastq *.temp.mate2.fastq *.generator.V2.overlap.fastq *.generator.V2.overlap.fastqd *.generator.V2.overlap.hashcount.fastq *.generator.V2.overlap.hashcount.fastq.bam.vcf *.generator.V2.overlap.hashcount.fastq.bam.vcf.bed;
echo "Cleanup done";
exit 1;
;;
*)
echo "ERROR: Unkown argument $1";
exit 100
_positionals+=("$1")
;;
esac
shift
done
}
assign_positional_args ()
{
_positional_names=()
_our_args=$((${#_positionals[@]} - ${#_positional_names[@]}))
for ((ii = 0; ii < _our_args; ii++))
do
_positional_names+=("_arg_exclude[$((ii + 0))]")
done
for (( ii = 0; ii < ${#_positionals[@]}; ii++))
do
eval "${_positional_names[ii]}=\${_positionals[ii]}" || die "Error during argument parsing, possibly an Argbash bug." 1
done
}
parse_commandline "$@"
region_postfix=""
if [ ! -z "${_arg_region}" ]; then
formatted_region=$(echo "${_arg_region}" | tr : _ | tr - _)
region_postfix=".${formatted_region}"
fi
# [ <-- needed because of Argbash
##############################__Print out all parameters__#################################################
#echo "~~~~~~~~~~~~ printing out paramater values used in script ~~~~~~~~~~~~~~~~"
#echo " _arg_exclude=:"
# for each in "${_arg_exclude[@]}"
# do
# echo " $each"
# done
#echo " _arg_controls=:"
# arg_control_string=""
# for each in "${_arg_controls[@]}" #
# do #
# echo " $each"
# arg_control_string="$arg_control_string $each" #
# done
if [ "$_arg_dev_reporting" = "TRUE" ]; then
echo "Verbose developer reporting on..."
echo " _arg_subject=$_arg_subject"
echo " _arg_ref=$_arg_ref"
echo " _arg_threads=$_arg_threads"
echo " _arg_kmersize=$_arg_kmersize"
echo " _arg_min=$_arg_min"
echo " _arg_refhash=$_arg_refhash"
echo " _arg_saliva=$_arg_saliva"
echo " _arg_exome=$_arg_exome"
echo " _MaxAlleleSize=$_MaxAlleleSize"
echo " _arg_mosaic=$_arg_mosaic"
echo " _assemblySpeed=$_assemblySpeed"
echo " _parallel_jelly=$_parallel_jelly"
echo " _pairedEnd=$_pairedEnd"
echo " _arg_region=$_arg_region"
echo " _arg_filterK=$_arg_filterK"
echo " _arg_ParLowK=$_arg_ParLowK"
echo " _filterMinQ=$_filterMinQ"
echo " _arg_dev_file_output=$_arg_dev_file_output"
fi
##############################__CHECK_FOR_MANDATORY_PARAMS__#################################################
if [ -z $_arg_kmersize ]
then
echo "INFO: You did not profide a kmer size, running with the default 25"
_arg_kmersize="25"
#echo "You must provide a kmer size [--kmersize|-k] (we recommend a kmer size of 25)"
#echo "Killing run with non-zero exit status"
#kill -9 $$
fi
if [ -z $_arg_threads ]
then
echo "INFO: no thread argument given, running with all avaialble threads = $(nproc)";
_arg_threads=$(nproc);
fi
if [ -z $_arg_subject ]
then
echo "ERROR: you must provide a subject sample (sample you want to call variants in)"
kill -9 $$
fi
if [ ${#_arg_exclude[@]} -eq "0" ] && [ ${#_arg_controls[@]} -eq "0" ]
then
echo "You must provide RUFUS with at least one control or exclude sample"
echo "Killing run with non-zero exit status"
kill -9 $$
fi
#########__remove -e and --exclude from _arg_exclude array__################
new_array=()
for value in "${_arg_exclude[@]}"
do
[[ $value != --exclude ]] && new_array+=($value)
done
ExcludeTemp=("${new_array[@]}")
unset new_array
new_array=()
for value in "${ExcludeTemp[@]}"
do
[[ $value != -e ]] && new_array+=($value)
done
_arg_exclude=("${new_array[@]}")
unset new_arary
unset ExcludeTemp
########################Setting up Exome Run EXPERIMENTAL ##################################
if [ "$_arg_exome" = "TRUE" ]; then
echo "Exome run set. Setting max kmer to 1M and saliva = true and making sure a lower cutoff was set "
MaxHashDepth=100000000
_arg_saliva="TRUE"
if [ -z $_arg_min ]; then
echo "Minimum not provided, picking a min of 20 for the alt count"
_arg_min="20"
fi
fi
#############################################################################################################
###############__PRINTING_OUT_ARG_BASH_VALUES__##############
#echo "Value of --subject: $_arg_subject" #
#echo "Value of --controls:" #
#for each in "${_arg_controls[@]}" #
#do #
# echo "$each" #
#done #
#echo "Value of --threads: $_arg_threads" #
#echo "Value of --kmersize: $_arg_kmersize" #
#echo "Value of --ref: $_arg_ref" #
#echo "Value of --minCount $_arg_min" #
#############################################################
Parents=("${_arg_controls[@]}")
_arg_ref_cat="${_arg_ref%.*}"
###############__CHECK_IF_ALL_REFERENCE_FILES_EXIST__#####################
BUILD_REFS="FALSE"
if [[ ! -e "$_arg_ref".sa ]] && [[ ! -e "$_arg_ref_cat".sa ]]
then
BUILD_REFS="TRUE"
fi
if [[ ! -e "$_arg_ref".bwt ]] && [[ ! -e "$_arg_ref_cat".bwt ]]
then
BUILD_REFS="TRUE"
fi
if [[ ! -e "$_arg_ref".pac ]] && [[ ! -e "$_arg_ref_cat".pac ]]
then
BUILD_REFS="TRUE"
fi
if [[ ! -e "$_arg_ref".amb ]] && [[ ! -e "$_arg_ref_cat".amb ]]
then
BUILD_REFS="TRUE"
fi
if [[ ! -e "$_arg_ref".ann ]] && [[ ! -e "$_arg_ref_cat".ann ]]
then
BUILD_REFS="TRUE"
fi
if [ "$BUILD_REFS" = "TRUE" ]; then
echo "Missing reference file indexes needed for BWA... Generating... "
fasta_idx=$(basename ${_arg_ref})
bwa index -a bwtsw $fasta_idx
samtools faidx $fasta_idx
fi
###### when we add PB need to check its reference stuff here
###########################################################################
refFileName=$(basename "$parent")
refExtension="${refFileName##*.}"
if [[ "$refExtension" != fa ]] && [[ -e "$_arg_ref".fa ]]
then
_arg_ref="$_arg_ref".fa
elif [[ "$refExtension" != fasta ]] && [[ -e "$_arg_ref".fasta ]]
then
_arg_ref="$_arg_ref".fasta
fi
if [[ ! -e "$_arg_ref" ]]
then
echo "cannot find reference file " "$_arg_ref"
echo "tried extensions: "
echo "no extension "
echo ".fa"
echo ".fasta"
echo "killing run with non-zero exit status"
kill -9 $$
fi
if [[ -e "$_arg_ref_cat".sa ]]
then
_arg_ref_bwa=$_arg_ref_cat
else
_arg_ref_bwa=$_arg_ref
fi
#echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
#echo "Reference supplied: " "$_arg_ref"
#echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
#########__CREATE_ALL_GENERATOR_FILES_AND_VARIABLES__#############
ProbandFileName=$(basename "$_arg_subject")
ProbandExtension="${ProbandFileName##*.}"
#echo "proband extension is $ProbandExtension"
######## checking proband extension, FASTQ is not handled, need to add that, for the meantime generator dumping to SAM needs to be used #############
if [[ "$ProbandExtension" != "cram" ]] && [[ "$ProbandExtension" != "bam" ]] || [[ ! -e "$_arg_subject" ]] && [[ "$ProbandExtension" != "generator" ]]
then
echo "The proband bam/generator file" "$_arg_subject" " was not provided or does not exist; killing run with non-zero exit status"
kill -9 $$
elif [[ "$ProbandExtension" == "bam" ]]
then
# echo "you provided the proband cram file" "$_arg_subject"
ProbandGenerator="${ProbandFileName}${region_postfix}.generator"
echo "samtools view -F 3328 $_arg_subject $_arg_region" > "$ProbandGenerator"
elif [[ "$ProbandExtension" == "cram" ]]
then
# echo "you provided the proband cram file" "$_arg_subject"
ProbandGenerator="${ProbandFileName}${region_postfix}.generator"
if [ "$_arg_cramref" == "" ]
then
echo "ERROR cram reference not provided for cram input";
kill -9 $$
fi
echo "samtools view -F 3328 -T $_arg_cramref $_arg_subject $_arg_region" > "$ProbandGenerator"
elif [[ "$ProbandExtension" = "generator" ]]
then
# echo "you provided the proband bam file" "$_arg_subject"
ProbandGenerator="${ProbandFileName}${region_postfix}"
else
echo "unknown error during generator generation, killing run with non-zero exit status"
fi
ParentGenerators=()
ParentJhash=()
ParentFileNames=""
space=" "
for parent in "${Parents[@]}"
do
parentFileName=$(basename "$parent")
ParentFileNames=$ParentFileNames$space$parent
parentExtension="${parentFileName##*.}"
if [[ "$parentExtension" != "cram" ]] && [[ "$parentExtension" != "bam" ]] && [[ "$parentExtension" != "generator" ]]
then
echo "The control bam/generator file" "$parent" " was not provided, or does not exist; killing run with non-zero exit status"
kill -9 $$
elif [[ "$parentExtension" == "bam" ]]
then
parentGenerator="${parentFileName}${region_postfix}.generator"
ParentGenerators+=("$parentGenerator")
echo "samtools view -F 3328 $parent $_arg_region" > "$parentGenerator"
# echo "You provided the control bam file" "$parent"
elif [[ "$parentExtension" == "cram" ]]
then
parentGenerator="${parentFileName}${region_postfix}.generator"
ParentGenerators+=("$parentGenerator")
if [ "$_arg_cramref" == "" ]
then
echo "ERROR cram reference not provided for cram input";
kill -9 $$
fi
echo "samtools view -F 3328 -T $_arg_cramref $parent $_arg_region" > "$parentGenerator"
# echo "You provided the control cram file" "$parent"
elif [[ "$parentExtension" = "generator" ]]
then
parentGenerator="${parentFileName}${region_postfix}"
ParentGenerators+=("$parentGenerator")
# echo "You provided the control bam file" "$parent"
fi
done
#################################################################
################__COPY_ARG_BASH_VARIABLES_TO_SCRIPT_VARIABLES__##################
K=$_arg_kmersize
Threads=$_arg_threads
ref=$_arg_ref
#################################################################################
if [[ -z "$K" ]]
then
echo "@@@@@@@@@@@__WARNING__@@@@@@@@@@@@@"
echo "kmer size ([-k|kmersize]) was not provided, killing run with non-zero exit status"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
kill -9 $$
fi
if [[ -z "$Threads" ]]
then
echo "@@@@@@@@@@@__WARNING__@@@@@@@@@@@@@"
echo "number of threads ([-t|--threads]) was not provided, killing run with non-zero exit status"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
kill -9 $$
fi
if [[ -z "$ref" ]]
then
echo "@@@@@@@@@@@__WARNING__@@@@@@@@@@@@@"
echo "reference file ([-r|--ref]) was not provided, killing run with non-zero exit status"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
kill -9 $$
fi
###################__PRINT_VARIABLES_USED__######################################
#echo "~~~~~~~~~~~~ printing out parameter values used in script ~~~~~~~~~~~~~~~~"
#echo "value of ProbandGenerator $ProbandGenerator"
#echo "Value of ParentGenerators:"
#for parent in "${ParentGenerators[@]}"
#do
# echo " $parent"
#done
#echo "Value of K is: $K"
#echo "Value of Threads is: $Threads"
#echo "value of ref is: $ref"
#echo "value of min is: $_arg_min"
#echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
#################################################################################
if [ "$_arg_refhash" ]
then
echo "Reference hash provided: " "$_arg_refhash"
fi
if [ "$_arg_min" ]
then
MutantMinCov=$_arg_min
fi
######################################
############__BUILD_JHASH_STRING__################
parentsString=""
parentsExcludeString=""
space=" "
jhash=".Jhash"
for parent in "${ParentGenerators[@]}"
do
#echo "parent is $parent "
parentsString=$parentsString$space$parent$jhash
done
for exclude in "${_arg_exclude[@]}"
do
parentsExcludeString=$parentsExcludeString$space$exclude
done
##################################################
##########################__SET_EXECUTABLE_PATHS__##############################
RUFUSmodel=$RDIR/bin/ModelDist
RUFUSfilter=$RDIR/bin/RUFUS.Filter
RufAlu=$RDIR/bin/externals/rufalu/src/rufalu_project/src/aluDetect
RUFUSOverlap=$RDIR/scripts/Overlap.shorter.sh
RunJelly=$RDIR/scripts/RunJellyForRUFUS.sh
PullSampleHashes=$RDIR/scripts/CheckJellyHashList.sh
RemoveCoInheritedVars=$RDIR/scripts/remove_coinherited.sh
modifiedJelly=$RDIR/bin/externals/modified_jellyfish/src/modified_jellyfish_project/bin/jellyfish
bwa=$RDIR/bin/externals/bwa/src/bwa_project/bwa
RUFUSfilterFASTQ=$RDIR/bin/RUFUS.Filter
RUFUSfilterFASTQse=$RDIR/bin/RUFUS.Filter.single
fastp=$RDIR/bin/externals/fastp/src/fastp_project/fastp
samblaster=$RDIR/bin/externals/samblaster/src/samblaster_project/samblaster
############################################################################################
####################__GENERATE_JHASH_FILES_FROM_JELLYFISH__#####################
if [ $_parallel_jelly == "yes" ]
then
######## TODO instead of assuming 3 samples
JThreads=$(( Threads / 3 ))
if [ "$JThreads" -lt 3 ]
then
JThreads=3
fi
#JThreads=$Threads
for parent in "${ParentGenerators[@]}"
do
bash $RunJelly $parent $K $(echo $JThreads -2 | bc) $_arg_ParLowK &
done
bash $RunJelly $ProbandGenerator $K $(echo $JThreads -2 | bc) 2 &
wait
else
JThreads=$Threads
if [ "$JThreads" -lt 3 ]
then
JThreads=3
fi
for parent in "${ParentGenerators[@]}"
do
bash $RunJelly $parent $K $(echo $JThreads -2 | bc) $_arg_ParLowK
done
# bash $RunJelly $ProbandGenerator $K $Threads 2
bash $RunJelly $ProbandGenerator $K $(echo $JThreads -2 | bc) 2
fi
##############################################################################
###########################_EMPTY_JHASH_CHECK##############################
########TODO just checking file size isn't a great idea, when jellyfish fails the fields arent zero size
for parent in "${ParentGenerators[@]}"
do
## Check Jhash files are not empty
if [ ! -s "$parent".Jhash ]
then
echo "@@@@@@@@@@@__WARNING__@@@@@@@@@@@@@"
echo "$parent.Jhash is empty"
echo "Killing run with exit status 1"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
kill -9 $$
fi
done
if [ ! -s "$ProbandGenerator".Jhash ]
then
echo "@@@@@@@@@@@__WARNING__@@@@@@@@@@@@@"
echo "$ProbandGenerator.Jhash is empty"
echo "Killing run with exit status 1"
echo "@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@"
kill -9 $$
fi
##############################################################################
##################__GENERATE_JHASH_HISTOGRAMS__#################################
######TODO I can probably get rid of this if I just make model read either tab or space
perl -ni -e 's/ /\t/;print' "$ProbandGenerator".Jhash.histo
for parent in "${ParentGenerators[@]}"
do
perl -ni -e 's/ /\t/;print' "$parent".Jhash.histo
done
##############################################################################
#######################__RUFUS_Model__############################################
#if [ $_arg_exome == "FALSE" ] #[ -z "$_arg_min" ]
if [ -z "$_arg_min" ] && [ $_arg_exome == "FALSE" ]
then
echo "No exome supplied, running whole genome mode" #echo "min not provided, building model"
if [ -e "$ProbandGenerator.Jhash.histo.7.7.model" ]
then
echo "Skipping model phase..."
else
echo "Starting model phase..."
"$RUFUSmodel" "$ProbandGenerator".Jhash.histo $K 150 $Threads > "$ProbandGenerator".Jhash.histo.7.7.out
for parent in "${ParentGenerators[@]}"
do
"$RUFUSmodel" "$parent".Jhash.histo $K 150 $Threads > "$parent".Jhash.histo.7.7.out &
done
echo "Model phase complete"
fi
if [ -z "$_arg_min" ]
then
if [ -e "$ProbandGenerator".Jhash.histo.7.7.model ]
then
if [ "$_arg_dev_reporting" = "TRUE" ]; then
echo "$(grep Best\ Model "$ProbandGenerator".Jhash.histo.7.7.out)"
fi
MutantMinCov=$(head -2 "$ProbandGenerator".Jhash.histo.7.7.model | tail -1 )
if [ "$_arg_dev_reporting" = "TRUE" ]; then
echo "INFO: mutant min coverage from generated model is $MutantMinCov"
fi
MutantSC=$(head -4 "$ProbandGenerator".Jhash.histo.7.7.model | tail -1 )
if [ "$_arg_dev_reporting" = "TRUE" ]; then
echo "INFO: mutant SC coverage from generated model is $MutantSC"
fi
MaxHashDepth=$(echo "$MutantSC * 5" | bc)
if [ "$_arg_dev_reporting" = "TRUE" ]; then
echo "INFO: MaxHashDepth = $MaxHashDepth"
fi
else
echo "ERROR Model didnt run correctly, exiting"
return -1
fi
else
echo "min coverage provided of $_arg_min, setting min kmer to that"
MutantMinCov="$_arg_min"
fi
else
if [ -z "$_arg_min" ]
then
echo "min coverage must be provided with an exome run"
return -1;
else
####TODO: check what im done here
echo "3" > "$ProbandGenerator".Jhash.histo.7.7.model;
echo "$_arg_min" >> "$ProbandGenerator".Jhash.histo.7.7.model;
echo "3.1392e+09" >> "$ProbandGenerator".Jhash.histo.7.7.model;
echo "1000000" >> "$ProbandGenerator".Jhash.histo.7.7.model;
echo "min was provided, min is $_arg_min"
MutantMinCov="$_arg_min"
#touch "$ProbandGenerator".Jhash.histo.7.7.model
fi
fi
########################################################################################
if [ "$_arg_stop" = "jelly" ];
then
echo "-StJ used, stopping run";
exit 1;
fi
#######################################################################################
if [ -z $MutantMinCov ]; then
echo "ERROR: No min coverage set, possible error in Model"
exit 100
fi
if [ "$MutantMinCov" -lt "2" ]
then
echo "ERROR, model couldn't pick a sensible lower cutoff, check your subject bam file"
exit
fi
#################################__HASH_LIST_FILTER__#####################################
echo "Identifying unique subject kMers..."
if [ -s "$ProbandGenerator".k"$K"_c"$MutantMinCov".HashList ]
then
echo "$ProbandGenerator.HashList exists, skipping creation..."
else
if [ -e "$ProbandGenerator".temp ]
then
rm "$ProbandGenerator".temp
fi
mkfifo "$ProbandGenerator".temp
$modifiedJelly merge -o "${ProbandGenerator}.mer_counts_merged.jf" "$ProbandGenerator".Jhash $(echo $parentsString) $(echo $parentsExcludeString) > "$ProbandGenerator".temp &
bash $PullSampleHashes $ProbandGenerator.Jhash "$ProbandGenerator".temp $MutantMinCov $MaxHashDepth > "$ProbandGenerator".k"$K"_c"$MutantMinCov".HashList
wait
fi
########################################################################################
if [ $(head "$ProbandGenerator".k"$K"_c"$MutantMinCov".HashList | wc -l | awk '{print $1}') -eq "0" ]; then
echo "ERROR: No mutant hashes identified, either the files are exactly the same of something went wrong in previous step"
exit 100
fi
########################################################################################
if [ "$_arg_stop" = "hash" ];
then
echo "-StH used, stopping run";
exit 1;
fi
######################__RUFUS_FILTER__##################################################
echo "Filtering unique kMers..."
if [ $_pairedEnd == "true" ]
then
if [ -e "$ProbandGenerator".Mutations.Mate1.fastq ]
then
echo "skipping filter"
else
if [ -z $_arg_fastqA ]
then
if [ -e "$ProbandGenerator".temp.mate1.fastq ]; then
rm "$ProbandGenerator".temp.mate1.fastq
fi
if [ -e "$ProbandGenerator".temp.mate2.fastq ]; then
rm "$ProbandGenerator".temp.mate2.fastq
fi
if [ -e "$ProbandGenerator".temp ]; then
rm "$ProbandGenerator".temp
fi
#echo "running this one "
mkfifo "$ProbandGenerator".temp.mate1.fastq "$ProbandGenerator".temp.mate2.fastq
sleep 1
bash "$ProbandGenerator" | "$RDIR"/bin/PassThroughSamCheck.stranded "$ProbandGenerator".filter.chr "$ProbandGenerator".temp > "$ProbandGenerator".temp &
$RUFUSfilterFASTQ "$ProbandGenerator".k"$K"_c"$MutantMinCov".HashList "$ProbandGenerator".temp.mate1.fastq "$ProbandGenerator".temp.mate2.fastq "$ProbandGenerator" "$K" $_filterMinQ $_arg_filterK "$(echo $Threads -2 | bc)" &
wait
else
echo "Running RUFUS.filter from paired FASTQ files"
FileName=$(basename $_arg_fastqA)
Extension="${FileName##*.}"
if [[ $Extension == 'gz' ]]
then
echo "Compressed fastq files found"
$RUFUSfilterFASTQ "$ProbandGenerator".k"$K"_c"$MutantMinCov".HashList <(zcat $_arg_fastqA) <(zcat $_arg_fastqB) "$ProbandGenerator" $K $_filterMinQ $_arg_filterK "$(echo $Threads -2 | bc)"
else