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executionMethods.bash
executable file
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/
executionMethods.bash
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if [[ "$@" =~ "--debug" ]]; then
set -ex
else
set -e
fi
invalidband=1
cfileband=0
statusband=0
rfileband=0
dbm2band=0
dbmxband=0
mxnamesband=0
psfilterdb=0
dbmarkerband=0
sigmacfileband=0
csfileband=0
dbsgband=0
dbtaxatorband=0
dbrawtaxatorband=0
taxatortaxband=0
priorband=0
PSFDB=""
TOCLEAN=""
SIGMACFILE=""
TMPNAME="TMP_FOLDER"
INITIALPATH=$(pwd)
for i in "$@"
do
case $i in
"--cfile")
cfileband=1
invalidband=0
;;
"--rfile")
rfileband=1
invalidband=0
;;
"--PSfilterdb")
psfilterdb=1
invalidband=0
;;
"--dbM2")
dbm2band=1
invalidband=0
;;
"--dbmarker")
dbmarkerband=1
invalidband=0
;;
"--dbMX")
dbmxband=1
invalidband=0
;;
"--MXnames")
mxnamesband=1
invalidband=0
;;
"--sigmacfile")
sigmacfileband=1
invalidband=0
;;
"--dbSG")
dbsgband=1
invalidband=0
;;
"--dbTX")
dbtaxatorband=1
invalidband=0
;;
"--dbTXraw")
dbrawtaxatorband=1
invalidband=0
;;
"--TXtax")
taxatortaxband=1
invalidband=0
;;
"--csfile")
csfileband=1
invalidband=0
;;
"--tprior")
priorband=1
invalidband=0
;;
"--help")
invalidband=0
echo "#########################################################################################"
printf "\nUsage: bash executionMethods --cfile [config file] --rfile [readsfile] -[DB options] [databases]"
printf "\nOptions aviable:"
echo "--cfile configuration file check README for more information"
echo "--rfile reads file, if you have paired end reads, use: --rfile readfile1.fa,readfile2.fa"
echo "--PSfilterdb pathoscope filter databases prefix"
echo "--dbmarker is the pkl file used by metaphlan, if you don't use metaphlan, don't use this flag (full path)"
echo "--sigmacfile is the configuration file used by sigma, if in your cfile, SIGMA is in the METHODS flag, you must provide the sigmacfile"
echo "--tprior thetaPrior option of pathoscope"
printf "\nDB options:"
echo "--dbPS pathoscope database folder and prefix: e.g /home/user/dbpathoscope_bt2/targetdb (bowtie2 index)"
echo "--dbM2 metaphlan database folder and prefix: e.g /home/user/dbmarkers_bt2/targetdb (bowtie2 index)"
echo "--dbMX metamix database folder and prefix: e.g /home/user/dbmetamix_nhi/targetdb (blast index)"
echo "--MXnames metamix names translation, is a file with format 'ti name'"
echo "--dbSG sigma database folder (master directory)"
echo "--dbCS constrains database folder"
echo "note: you must provide sigma database folder in the sigma config file"
printf "\n#########################################################################################"
exit
;;
*)
if [ $((cfileband)) -eq 1 ];then
if ! [ -f $i ];then
echo "$i file no exist"
exit
fi
for parameter in $(awk '$0 !~ /^#/ {print}' $i |awk '{if($0!="")print}')
do
Pname=$(echo "$parameter" |awk -F"=" '{print $1}')
case $Pname in
"METHOD")
METHOD=$(echo "$parameter" | awk -F"=" '{print $2}' | sed "s/,/ /g")
;;
"CORES")
CORES=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"THREADS")
THREADS=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"PYTHONBIN")
PYTHONBIN=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"PATHOSCOPEHOME")
PATHOSCOPEHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"DBPS")
DBPS=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"DBPSDIR")
DBPSDIR=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"SIGMAHOME")
SIGMAHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"BLASTHOME")
BLASTHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"METAPHLAN2HOME")
METAPHLAN2HOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"CONSTRAINSHOME")
CONSTRAINSHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"SAMTOOLSHOME")
SAMTOOLSHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"BOWTIE2HOME")
BOWTIE2HOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"KRAKENHOME")
KRAKENHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"DBKR")
DBKR=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"TAXATORHOME")
TAXATORHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"TAXATORTK_TAXONOMY_NCBI")
TAXATORTK_TAXONOMY_NCBI=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"CENTRIFUGEHOME")
CENTRIFUGEHOME=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"CENTRIFUGEDB")
DBCF=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
"COORDFOLDER")
COORDFOLDER=$(echo "$parameter" | awk -F"=" '{print $2}')
;;
esac
done
if [ "$COORDFOLDER" == "" ];then
COORDFOLDER=$HOME
else
cd $COORDFOLDER
COORDFOLDER=$(pwd)
cd $OLDPWD
fi
statusband=$((statusband+1))
cfileband=0
fi
if [ $((rfileband)) -eq 1 ]; then
#first, we check if exist the pair end call.
IRFILE=$i
rfileband=0
READS=$(echo "$i" |awk 'BEGIN{FS=","}{if($2 == ""){print "single"}else{print "paired"}}')
fi
if [ $((dbm2band)) -eq 1 ]; then
if [ ! -f $METAPHLAN2HOME/metaphlan2.py ]; then
echo "metaphlan2.py no exist in $METAPHLAN2HOME"
exit
fi
ok=`ls -1 "$i"* |wc -l |awk '{print $1}'`
if [ $((ok)) -ge 1 ]; then
DBM2=`echo "$i" |rev |cut -d "/" -f 1 |rev`
M2IXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $M2IXDIR
dbpath=`pwd`
DBM2=`echo "$dbpath/$DBM2"`
dbm2band=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((dbmxband)) -eq 1 ]; then
ok=`ls -1 "$i"* |wc -l |awk '{print $1}'`
if [ $((ok)) -ge 1 ]; then
DBMX=`echo "$i" |rev |cut -d "/" -f 1 |rev`
MXIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $MXIXDIR
dbpath=`pwd`
DBMX=`echo "$dbpath/$DBMX"`
dbmxband=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((mxnamesband)) -eq 1 ]; then
if [ -f "$i" ]; then
MXNAMES=`echo "$i" |rev |cut -d "/" -f 1 |rev`
MXNIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $MXNIXDIR
dbpath=`pwd`
MXNAMES=`echo "$dbpath/$MXNAMES"`
mxnamesband=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((psfilterdb)) -eq 1 ]; then
ok=`ls -1 "$i"* |wc -l |awk '{print $1}'`
if [ $((ok)) -ge 1 ]; then
PSFDB=`echo "$i" |rev |cut -d "/" -f 1 |rev`
PSFIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $PSFIXDIR
dbpath=`pwd`
PSFDB=`echo "$dbpath/$PSFDB"`
psfilterdb=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((dbmarkerband)) -eq 1 ]; then
if [ -f $i ]; then
DBMARKER=`echo "$i" |rev |cut -d "/" -f 1 |rev`
M2MIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $M2MIXDIR
dbpath=`pwd`
DBMARKER=`echo "$dbpath/$DBMARKER"`
dbmarkerband=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((sigmacfileband)) -eq 1 ]; then
if [ -f $i ]; then
SIGMACFILE=`echo "$i" |rev |cut -d "/" -f 1 |rev`
SGIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $SGIXDIR
dbpath=`pwd`
SIGMACFILE=`echo "$dbpath/$SIGMACFILE"`
sigmacfileband=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((dbsgband)) -eq 1 ]; then
if [ -d $i ]; then
cd $i
DBSG=`pwd`
dbsgband=0
cd $INITIALPATH
else
echo "$i master directory no exist"
exit
fi
fi
if [ $((csfileband)) -eq 1 ]; then
if [ -f $i ]; then
CSFILE=`echo "$i" |rev |cut -d "/" -f 1 |rev`
CSIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $CSIXDIR
dbpath=`pwd`
CSFILE=`echo "$dbpath/$CSFILE"`
csfileband=1
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((dbtaxatorband)) -eq 1 ]; then
ok=`ls -1 "$i"* |wc -l |awk '{print $1}'`
if [ $((ok)) -ge 1 ]; then
DBTX=`echo "$i" |rev |cut -d "/" -f 1 |rev`
TXIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $TXIXDIR
dbpath=`pwd`
DBTX=`echo "$dbpath/$DBTX"`
dbtaxatorband=0
cd $INITIALPATH
else
echo "$i file no exist"
exit
fi
fi
if [ $((taxatortaxband)) -eq 1 ]; then
if [ -f "$i" ]; then
TXTAX=`echo "$i" |rev |cut -d "/" -f 1 |rev`
TXTAXIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $TXTAXIXDIR
dbpath=`pwd`
TXTAX=`echo "$dbpath/$TXTAX"`
taxatortaxband=0
cd $INITIALPATH
else
echo "$i taxator tax file no exist"
exit
fi
fi
if [ $((dbrawtaxatorband)) -eq 1 ]; then
if [ -f "$i" ]; then
DBTXR=`echo "$i" |rev |cut -d "/" -f 1 |rev`
TXRIXDIR=`echo "$i" |rev |cut -d "/" -f 2- |rev`
cd $TXRIXDIR
dbpath=`pwd`
DBTXR=`echo "$dbpath/$DBTXR"`
dbrawtaxatorband=0
cd $INITIALPATH
else
echo "$i taxator tax file no exist"
exit
fi
fi
if [ $((priorband)) -eq 1 ]; then
PRIOR=$i
priorband=0
fi
if [ $((invalidband)) -eq 1 ]; then
echo "some of your parameters are invalid"
exit
else
invalid=1
fi
;;
esac
done
#################################################
declare pids
pindex=0
maxexe=$CORES
#################################################
lastpid=0
function coresControlFunction {
request=$1
if mkdir $COORDFOLDER/lockfolder_donttouch > /dev/null 2>&1; then
echo "coresControlFunction called by $2"
if [ -f "$COORDFOLDER"/corescontrol ]; then
i=$(tail -n1 $COORDFOLDER/corescontrol)
else
touch $COORDFOLDER/corescontrol
i=0
fi
if [ -f $COORDFOLDER/proccesscontrol ];then
firstproc=$(head -n1 $COORDFOLDER/proccesscontrol |awk '{print $1}')
firstcore=$(head -n1 $COORDFOLDER/proccesscontrol |awk '{print $2}')
else
firstproc="foo_proccess_foo"
touch $COORDFOLDER/proccesscontrol
fi
if [ $((i)) -ge $((maxexe)) ]; then
while [[ ( -d /proc/"$firstproc" ) && ( -z "grep zombie /proc/$firstproc/status" ) ]]; do
#echo "waiting for proccess $firstproc"
sleep 61
done
sed "1d" $COORDFOLDER/proccesscontrol >toreplace
rm $COORDFOLDER/proccesscontrol
mv toreplace $COORDFOLDER/proccesscontrol
sed "1d" $COORDFOLDER/corescontrol >toreplace
rm $COORDFOLDER/corescontrol
mv toreplace $COORDFOLDER/corescontrol
i=$(echo "$i $firstcore" |awk '{print $1-$2}')
echo "$i" >> "$COORDFOLDER"/corescontrol
else
echo "$request $i" |awk -v maxexe=$maxexe '{if($1+$2>=maxexe){print maxexe}else{print $1+$2}}' >>$COORDFOLDER/corescontrol
fi
else
sleep 60
coresControlFunction $request
fi
}
function coresunlockFunction {
rm -rf $COORDFOLDER/lockfolder_donttouch
}
function fastalockFunction {
if mkdir fastalock > /dev/null 2>&1; then
echo "fastalock created by $1"
else
sleep 60
fastalockFunction
fi
}
function fastaunlockFunction {
rm -rf fastalock
echo "fastalock removed"
}
function readstoFastqFunction {
if [ "$READS" == "paired" ]; then
PAIREND1=$(echo "$IRFILE" |awk -F"," '{print $1}')
NAMEP=$(echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev)
DIRP=$(echo "$PAIREND1" |rev |cut -d "/" -f 2- |rev)
cd $DIRP
PAIREND1=$(pwd |awk -v name=$NAMEP '{print $1"/"name}')
cd $OLDPWD
PAIREND2=$(echo "$IRFILE" |awk -F"," '{print $2}')
NAMEP=$(echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev)
DIRP=$(echo "$PAIREND2" |rev |cut -d "/" -f 2- |rev)
cd $DIRP
PAIREND2=$(pwd |awk -v name=$NAMEP '{print $1"/"name}')
cd $OLDPWD
arefastq=$(echo $PAIREND1 |awk -F"." '{print $NF}' )
if [ "$arefastq" == "fastq" ] || [ "$arefastq" == "fq" ];then
echo "files are in fastq, nice :D"
RFILE=$IRFILE
NAMEPAIREND1=$(echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev)
NAMEPAIREND2=$(echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev)
return 0
fi
#next, check the files (tolerance to missing files)
if [ -f "$PAIREND1" ];then
if [ -f "$PAIREND2" ];then
NAMEPAIREND1=$(echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev)
NAMEPAIREND2=$(echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev)
fastalockFunction $1
fasta_to_fastqFunction
if [ ! -f $TMPNAME/$NAMEPAIREND1.fastq ];then
perl fasta_to_fastq.pl $PAIREND1 > $TMPNAME/$NAMEPAIREND1.fastq
perl fasta_to_fastq.pl $PAIREND2 > $TMPNAME/$NAMEPAIREND2.fastq
fi
rm -f fasta_to_fastq.pl
fastaunlockFunction
RFILE=$(echo "$NAMEPAIREND1.fastq,$NAMEPAIREND2.fastq")
else
echo "$PAIREND2 doesn't exist"
exit
fi
else
echo "$PAIREND1 doesn't exist"
exit
fi
else
fastalockFunction $1
if [ -f fasta_to_fastq.pl ]; then
if [ ! -f $TMPNAME/$SINGLE.fastq ];then
perl fasta_to_fastq.pl $IRFILE > $TMPNAME/$SINGLE.fastq
RFILE=$SINGLE.fastq
fi
else
fasta_to_fastqFunction
if [ ! -f $TMPNAME/$SINGLE.fastq ];then
perl fasta_to_fastq.pl $IRFILE > $TMPNAME/$SINGLE.fastq
RFILE=$SINGLE.fastq
fi
fi
fastaunlockFunction
fi
}
function pathoscopeFunction {
echo "Wake up pathoscope2"
FILE=$IRFILE
readstoFastqFunction "pathoscope2"
cd $TMPNAME
coresControlFunction 1 "Pathoscope2 F1"
if [ "$PSFDB" == "" ];then
${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py MAP -1 $PAIREND1 -2 $PAIREND2 -indexDir $DBPSDIR -targetIndexPrefixes $DBPS -outDir . -outAlign pathoscope_$NAMEPAIREND1.$NAMEPAIREND2.sam -expTag MAPPED_$NAMEPAIREND1.$NAMEPAIREND2 -numThreads $THREADS -btHome $BOWTIE2HOME
# { time -p ${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py MAP -U $RFILE -indexDir $DBPSDIR -targetIndexPrefixes $DBPS -outDir . -outAlign pathoscope_$NAMEPAIREND1.$NAMEPAIREND2.sam -expTag MAPPED_$NAMEPAIREND1.$NAMEPAIREND2 -numThreads $THREADS 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > TimePSf1_$NAMEPAIREND1.$NAMEPAIREND2 &
lastpid=$!
SAMFILE=pathoscope_$NAMEPAIREND1.$NAMEPAIREND2.sam
else
{ time ${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py MAP -U $RFILE -indexDir $DBPSDIR -targetIndexPrefixes $DBPS -filterIndexPrefixes $PSFDB -outDir . -outAlign pathoscope_$NAMEPAIREND1.NAMEPAIREND2.sam -expTag MAPPED_$NAMEPAIREND1.NAMEPAIREND2 -numThreads $THREADS 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > TimePSf1_$NAMEPAIREND1.$NAMEPAIREND2 &
lastpid=$!
SAMFILE=pathoscope_$NAMEPAIREND1.$NAMEPAIREND2.sam
fi
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 pathoscopeF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
TOCLEAN=$RFILE
IRFILE=$FILE
}
function metaphlanFunction {
FILE=$IRFILE
echo "Wake up metaphlan2"
readstoFastqFunction "metaphlan2"
cd $TMPNAME
coresControlFunction 1 "Metaphlan2 F1"
if [ -f "bowtieout$RFILE.bz2" ];then
rm -f bowtieout$RFILE.bz2
fi
${PYTHONBIN} ${METAPHLAN2HOME}/metaphlan2.py $RFILE --input_type fastq --mpa_pkl $DBMARKER --bowtie2db $DBM2 --bowtie2out bowtieout$NAMEPAIREND1.$NAMEPAIREND2.bz2 --nproc $CORES > ../metaphlan_$NAMEPAIREND1.$NAMEPAIREND2.dat
# { time -p ${PYTHONBIN} ${METAPHLAN2HOME}/metaphlan2.py $RFILE --input_type fastq --mpa_pkl $DBMARKER --bowtie2db $DBM2 --bowtie2out bowtieout$NAMEPAIREND1.$NAMEPAIREND2.bz2 --nproc $CORES > ../metaphlan_$NAMEPAIREND1.$NAMEPAIREND2.dat ; } 2>&1 |grep "real" |awk '{print $2}' > TimeM2_$NAMEPAIREND1.$NAMEPAIREND2 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 metaphlanF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
TOCLEAN=$RFILE
IRFILE=$FILE
}
function metamixFunction {
echo "Wake up metamix"
if [ "$READS" == "paired" ]; then
PAIREND1=$(echo "$IRFILE" |awk 'BEGIN{FS=","}{print $1}')
PAIREND2=$(echo "$IRFILE" |awk 'BEGIN{FS=","}{print $2}')
#next, check the files (tolerance to missing files)
if [ -f "$PAIREND1" ];then
if [ -f "$PAIREND2" ];then
P1=`echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev`
P2=`echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev`
if mkdir $TMPNAME/metamix_$P1.$P2 1>/dev/null; then #we make new folder because is easier to clean after execution
echo "folder metamix_$P1.$P2 created"
else
echo "Metamix: cleaning previous run"
rm -r $TMPNAME/metamix_$P1.$P2
mkdir $TMPNAME/metamix_$P1.$P2
fi
cd $TMPNAME
cd metamix_$P1.$P2
coresControlFunction 1 "Metamix F1_1"
${BLASTHOME}/bin/blastn -query $PAIREND1 -outfmt "6 qacc qlen sseqid slen mismatch bitscore length pident evalue staxids" -db $DBMX -num_threads $THREADS > blastOut$P1.tab
# { time -p ${BLASTHOME}/bin/blastn -query $PAIREND1 -outfmt "6 qacc qlen sseqid slen mismatch bitscore length pident evalue staxids" -db $DBMX -num_threads $THREADS > blastOut$P1.tab ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeMXf1_$P1 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 metamixF1_1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
coresControlFunction 1 "Metamix F1_2"
${BLASTHOME}/bin/blastn -query $PAIREND2 -outfmt "6 qacc qlen sseqid slen mismatch bitscore length pident evalue staxids" -db $DBMX -num_threads $THREADS > blastOut$P2.tab
# { time -p ${BLASTHOME}/bin/blastn -query $PAIREND2 -outfmt "6 qacc qlen sseqid slen mismatch bitscore length pident evalue staxids" -db $DBMX -num_threads $THREADS > blastOut$P2.tab ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeMXf1_$P2 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 metamixF1_2" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
else
echo "$PAIREND2 no exist"
exit
fi
else
echo "$PAIREND1 no exist"
exit
fi
else
SINGLE=`echo "$IRFILE" |rev |cut -d "/" -f 1 |rev`
if mkdir $TMPNAME/metamix_$SINGLE 1>/dev/null; then #we make new folder because is easier to clean after execution
echo "folder metamix_$SINGLE created"
else
echo "Metamix: cleaning previous run"
rm -r $TMPNAME/metamix_$SINGLE
mkdir $TMPNAME/metamix_$SINGLE
fi
cd $TMPNAME
cd metamix_$SINGLE
coresControlFunction 1 "Metamix F1"
${BLASTHOME}/bin/blastn -query $IRFILE -outfmt "6 qacc qlen sseqid slen mismatch bitscore length pident evalue staxids" -db $DBMX -num_threads $THREADS > blastOut$SINGLE.tab
# { time -p ${BLASTHOME}/bin/blastn -query $IRFILE -outfmt "6 qacc qlen sseqid slen mismatch bitscore length pident evalue staxids" -db $DBMX -num_threads $THREADS > blastOut$SINGLE.tab ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeMXf1_$SINGLE &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid $CORES metamixF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
fi
}
function sigmaFunction {
echo "Wake up sigma"
cd $TMPNAME
coresControlFunction 1 "Sigma F1"
if [ "$RTYPE" == "PAIRED" ];then
SGTOCLEAN=sigma_$RFILE
if mkdir $SGTOCLEAN > /dev/null 2>&1;then
cd $SGTOCLEAN
else
echo "sigma: cleaning previous run"
rm -rf $SGTOCLEAN
mkdir $SGTOCLEAN
cd $SGTOCLEAN
fi
else
SGTOCLEAN=sigma_$RFILE
if mkdir $SGTOCLEAN > /dev/null 2>&1;then
cd $SGTOCLEAN
else
echo "sigma: cleaning previous run"
rm -rf $SGTOCLEAN
mkdir $SGTOCLEAN
cd $SGTOCLEAN
fi
fi
mv ../$SIGMACFILE .
# { time -p ${SIGMAHOME}/bin/sigma-align-reads -c $SIGMACFILE -w . 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > TimeSGf1_$NAMEPAIREND1.$NAMEPAIREND2 &
${SIGMAHOME}/bin/sigma-align-reads -c $SIGMACFILE -w .
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 sigmaF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
}
function krakenFunction {
echo "Wake up kraken"
cd $TMPNAME
if [ "$READS" == "paired" ]; then
PAIREND1=$(echo "$IRFILE" |awk -F"," '{print "../"$1}')
PAIREND2=$(echo "$IRFILE" |awk -F"," '{print "../"$2}')
#next, check the files (tolerance to missing files)
if [ -f "$PAIREND1" ];then
if [ -f "$PAIREND2" ];then
P1=$(echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev)
P2=$(echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev)
coresControlFunction 1 "Kraken F1"
${KRAKENHOME}/kraken --db $DBKR --paired $PAIREND1 $PAIREND2 --threads $THREADS --preload > kraken_$P1.$P2.kraken
# { time -p ${KRAKENHOME}/kraken --db $DBKR --paired $PAIREND1 $PAIREND2 --threads $THREADS --preload > kraken_$P1.$P2.kraken ; } 2>&1 |grep "real" |awk '{print $2}' > TimeKRf1_$P1.$P2 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 krakenF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
else
echo "$PAIREND2 no exist"
exit
fi
else
echo "$PAIREND1 no exist"
exit
fi
else
coresControlFunction 1 "Kraken F1"
SINGLE=$(echo "$IRFILE" |rev |cut -d "/" -f 1 |rev)
${KRAKENHOME}/kraken --db $DBKR ../$IRFILE --threads $THREADS --preload > kraken_$SINGLE.kraken
# { time -p ${KRAKENHOME}/kraken --db $DBKR ../$IRFILE --threads $THREADS --preload > kraken_$SINGLE.kraken ; } 2>&1 |grep "real" |awk '{print $2}' > TimeKRf1_$SINGLE &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 krakenF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
fi
cd ..
}
function taxatorFunction {
echo "Wake up taxator-tk"
if [ "$READS" == "paired" ]; then
PAIREND1=`echo "$IRFILE" |awk 'BEGIN{FS=","}{print $1}'`
PAIREND2=`echo "$IRFILE" |awk 'BEGIN{FS=","}{print $2}'`
#next, check the files (tolerance to missing files)
if [ -f "$PAIREND1" ];then
if [ -f "$PAIREND2" ];then
P1=$(echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev)
P2=$(echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev)
if mkdir $TMPNAME/taxator_$P1.$P2 1>/dev/null; then #we make new folder because is easier to clean after execution
echo "folder taxator_$P1.$P2 created"
else
echo "Taxator: cleaning previous run"
rm -r $TMPNAME/taxator_$P1.$P2
mkdir $TMPNAME/taxator_$P1.$P2
fi
cd $TMPNAME
cd taxator_$P1.$P2
coresControlFunction 1 "Taxator F1_1"
${BLASTHOME}/bin/blastn -query $PAIREND1 -outfmt '6 qseqid qstart qend qlen sseqid sstart send bitscore evalue nident length' -db $DBTX -num_threads $THREADS > blastOut$P1.tab
# { time -p ${BLASTHOME}/bin/blastn -query $PAIREND1 -outfmt '6 qseqid qstart qend qlen sseqid sstart send bitscore evalue nident length' -db $DBTX -num_threads $THREADS > blastOut$P1.tab ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeTXf1_$P1 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 taxatorF1_1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
coresControlFunction 1 "Taxator F1_2"
${BLASTHOME}/bin/blastn -query $PAIREND2 -outfmt '6 qseqid qstart qend qlen sseqid sstart send bitscore evalue nident length' -db $DBTX -num_threads $THREADS > blastOut$P2.tab
# { time -p ${BLASTHOME}/bin/blastn -query $PAIREND2 -outfmt '6 qseqid qstart qend qlen sseqid sstart send bitscore evalue nident length' -db $DBTX -num_threads $THREADS > blastOut$P2.tab ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeTXf1_$P2 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 taxatorF1_2" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
else
echo "$PAIREND2 no exist"
exit
fi
else
echo "$PAIREND1 no exist"
exit
fi
else
SINGLE=$(echo "$IRFILE" |rev |cut -d "/" -f 1 |rev)
if mkdir $TMPNAME/taxator_$SINGLE 1>/dev/null; then #we make new folder because is easier to clean after execution
echo "folder taxator_$SINGLE created"
else
echo "Taxator: cleaning previous run"
rm -r $TMPNAME/taxator_$SINGLE
mkdir $TMPNAME/taxator_$SINGLE
fi
cd $TMPNAME
cd taxator_$SINGLE
coresControlFunction $CORES "Taxator F1"
${BLASTHOME}/bin/blastn -query $IRFILE -outfmt '6 qseqid qstart qend qlen sseqid sstart send bitscore evalue nident length' -db $DBTX -num_threads $THREADS > blastOut$SINGLE.tab
# { time -p ${BLASTHOME}/bin/blastn -query $IRFILE -outfmt '6 qseqid qstart qend qlen sseqid sstart send bitscore evalue nident length' -db $DBTX -num_threads $THREADS > blastOut$SINGLE.tab ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeMXf1_$SINGLE &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid $CORES taxatorF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
fi
}
function centrifugeFunction {
echo "Wake up centrifuge"
readstoFastqFunction "Centrifuge"
if [ "$READS" == "paired" ]; then
P1=$(echo "$PAIREND1" |rev |cut -d "/" -f 1 |rev)
P2=$(echo "$PAIREND2" |rev |cut -d "/" -f 1 |rev)
if mkdir $TMPNAME/centrifuge_$P1.$P2 1>/dev/null; then #we make new folder because is easier to clean after execution
echo "folder centrifuge_$P1.$P2 created"
else
echo "Centrifuge: cleaning previous run"
rm -r $TMPNAME/centrifuge_$P1.$P2
mkdir $TMPNAME/centrifuge_$P1.$P2
fi
cd $TMPNAME
cd centrifuge_$P1.$P2
coresControlFunction $CORES "Centrifuge F1"
${CENTRIFUGEHOME}/bin/centrifuge -p $CORES -x $DBCF -1 $PAIREND1 -2 $PAIREND2 > centrifuge_$P1.$P2.tsv
# { time -p ${CENTRIFUGEHOME}/bin/centrifuge -p $CORES -x $DBCF -1 $PAIREND1 -2 $PAIREND2 > centrifuge_$P1.$P2.tsv ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeCF_$P1.$P2 &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid $CORES centrifugeF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
else
SINGLE=$(echo "$RFILE" |rev |cut -d "/" -f 1 |rev)
if mkdir $TMPNAME/centrifuge_$SINGLE 1>/dev/null; then #we make new folder because is easier to clean after execution
echo "folder centrifuge_$SINGLE created"
else
echo "Centrifuge: cleaning previous run"
rm -r $TMPNAME/centrifuge_$SINGLE
mkdir $TMPNAME/centrifuge_$SINGLE
fi
cd $TMPNAME
cd centrifuge_$SINGLE
coresControlFunction $CORES "Centrifuge F1"
${CENTRIFUGEHOME}/bin/centrifuge -p $CORES -x $DBCF ../../$SINGLE > centrifuge_$SINGLE.tsv
# { time -p ${CENTRIFUGEHOME}/bin/centrifuge -p $CORES -x $DBCF ../../$SINGLE > centrifuge_$SINGLE.tsv ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeCF_$SINGLE &
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid $CORES CentrifugeF1" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
cd ..
fi
}
function pathoscopeFunction2 {
echo "executing pathoscope ID module"
cd $TMPNAME
coresControlFunction 1 "Pathoscope2 F2"
if [ "$PRIOR" == "" ];then
${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py ID -alignFile $SAMFILE -fileType sam -outDir ../ -expTag $SAMFILE
# { time -p ${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py ID -alignFile $SAMFILE -fileType sam -outDir ../ -expTag $SAMFILE 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > TimePSf2_$NAMEPAIREND1.$NAMEPAIREND2 &
else
${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py ID -alignFile $SAMFILE -fileType sam -outDir ../ -expTag $SAMFILE -thetaPrior $PRIOR
# { time -p ${PYTHONBIN} ${PATHOSCOPEHOME}/pathoscope2.py ID -alignFile $SAMFILE -fileType sam -outDir ../ -expTag $SAMFILE -thetaPrior $PRIOR 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > TimePSf2_$NAMEPAIREND1.$NAMEPAIREND2 &
fi
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 pathoscopeF2" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
}
function metamixFunction2 {
cd $TMPNAME
coresControlFunction 12 "Metamix F2" #parallel tempering requires 12 cores
if [ "$READS" == "paired" ]; then
cat TimeMXf1_$P1 TimeMXf1_$P2 |awk 'BEGIN{sum=0}{sum+=$1}END{print sum}' > TimeMXf1_$P1.$P2
rm -f TimeMXf1_$P1 TimeMXf1_$P2
cd metamix_$P1.$P2
BACKUPNAME=$(echo "metamix_$P1.$P2")
metamixCodeFunction
echo "call to metamix R function"
cat blastOut$P1.tab blastOut$P2.tab > blastOut$P1.$P2.tab
rm blastOut$P1.tab blastOut$P2.tab
executionpath=$(pwd)
executeMetamix blastOut$P1.$P2.tab $executionpath
# { time -p executeMetamix blastOut$P1.$P2.tab $executionpath 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeMXf2_$P1.$P2 &
cd ..
else
cd metamix_$SINGLE
metamixCodeFunction
echo "execute metamix R function"
executionpath=$(pwd)
executeMetamix blastOut$SINGLE.tab $executionpath
# { time -p executeMetamix blastOut$SINGLE.tab $executionpath 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > ../TimeMXf2_$SINGLE &
cd ..
fi
lastpid=$!
pids[${pindex}]=$lastpid
pindex=$((pindex+1))
echo "$lastpid 1 metamixF2" >> $COORDFOLDER/proccesscontrol
coresunlockFunction
cd ..
}
function sigmaFunction2 {
cd $TMPNAME
cd $SGTOCLEAN
#Sigma don't allow several intances, so we set until 2 parallel instances
twoInstances=$(echo $CORES |awk '{print int($1/2)}')
coresControlFunction $twoInstances "Sigma F2"
echo "executing sigma wrapper module"
# { time -p ${SIGMAHOME}/bin/sigma -c $SIGMACFILE -t $THREADS -w . 1>/dev/null ; } 2>&1 |grep "real" |awk '{print $2}' > TimeSGf2_$RFILE &