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orderedPainting.sh
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#! /bin/bash
. lib/env_func.bashrc
usage () {
if [ "${QUEUE_TYPE}" == "SGE" ]; then
echo "qsub -cwd <<< '"
elif [ "${QUEUE_TYPE}" == "LSF" ]; then
echo "bsub -o logfile.txt <<< '"
elif [ "${QUEUE_TYPE}" == "SLURM" ]; then
echo "qsub -l walltime:01:00:00 -q standard -o logfile.txt $(basename $0)"
else
echo_fail "unknown QUEUE_TYPE: ${QUEUE_TYPE}"
fi
echo "/bin/bash $0 "
echo " -g file.hap "
echo " -l strainName.list (individual name in the hap file)"
echo " [-n 20 (num. of dirs where uncompressed tmp files are processed simultaneously: default=20) ]"
echo " [-t 10 (num. of orderings: default=10) ]"
echo " [-m pos_missingInd.txt (pos[tab]missing_individual_name) ]"
echo " [-o strainName.list (individual name in an order for output matrices: default is the file specified by -l) ]"
echo " [-x (output matrix files for top/middle/bottom sites) ]"
echo " [-s 1 (seed of random number generator: default=1) ]"
echo "' "
exit 1
}
################################################################################################################
#
# env
#
LIB_DIR=lib # created by setup.sh
LOG_DIR=log # created by setup.sh
EXE_PAINT=./${LIB_DIR}/chromopainter # also used in SH_PAINT_QSUB
PL_CHECK_LINE_LEN=./${LIB_DIR}/check_lineLen.pl
PL_MAKE_RECMAP=./${LIB_DIR}/makeuniformrecfile.pl
PL_ESTIMATE_Ne=./${LIB_DIR}/neaverage.pl
EXE_RANDOMIZE=./${LIB_DIR}/randomize/rd
SH_RANDOMIZE=./${LIB_DIR}/randomize_arrayjob.sh
SH_PAINT_QSUB=./${LIB_DIR}/chromopainter_linkage_orderings_arrayjob.sh
PL_SITE_BY_SITE=./${LIB_DIR}/create_examine_site_by_site_matrices.pl
SH_DECOMPRESS_SORT_SPLIT_EACH_ORDERING=./${LIB_DIR}/decompress_sort_split_gz_arrayjob.sh
PL_MSORT_EACH_ORDERING=./${LIB_DIR}/msort_each_ordering.pl
EXE_SORT=./${LIB_DIR}/sort
EXE_SPLITN=./${LIB_DIR}/splitN/sp
EXE_PP=./${LIB_DIR}/postprocess/pp
R_MAIN1=./${LIB_DIR}/visualization1.R
R_LIB_HEATMAP=./${LIB_DIR}/plotHeatmap.R
R_MAIN2=./${LIB_DIR}/visualization2.R
SH_R_MAIN2=./${LIB_DIR}/visualization2_arrayjob.sh
R_CHECK_MISSING_STAT=./${LIB_DIR}/check_missingCnt_distStat.R
# to check existence below
arr_executable_files=(
$EXE_PAINT
$PL_CHECK_LINE_LEN
$PL_MAKE_RECMAP
$PL_ESTIMATE_Ne
$EXE_RANDOMIZE
$SH_RANDOMIZE
$EXE_PAINT
$PL_SITE_BY_SITE
$SH_DECOMPRESS_SORT_SPLIT_EACH_ORDERING
$PL_MSORT_EACH_ORDERING
$EXE_SORT
$EXE_SPLITN
$EXE_PP
)
arr_R_files=(
$R_MAIN1
$R_MAIN2
$R_LIB_HEATMAP
$R_CHECK_MISSING_STAT
)
#
# constant
#
NUM_EM=30 # 0-indexed. 10 is sometimes not enough for convergence
NUM_SPLITN=9
#
# rule
#
GZ_CAT_COPYPROB_EACH_DIR=copyprobsperlocus.cat.gz
#
# vars
#
OUT_DIR=""
################################################################################################################
#
# func
# used only in this script
# other functions are defined in lib/env_func.bashrc
#
move_log_files() {
declare -a arr_logs
arr_logs=`find . -maxdepth 1 -name $1\*$2\* -print`
#if ls $1*$2* &> /dev/null; then
for each_log in ${arr_logs[@]}
do
if [ -f "${each_log}" ]; then
/bin/mv ${each_log} ${LOG_DIR}/
echo "log file ${each_log} was moved to ${LOG_DIR}/"
fi
done
}
returnQSUB_CMD() {
QSUB_CMD=""
if [ "${QUEUE_TYPE}" == "SGE" -o "${QUEUE_TYPE}" == "UGE" ]; then
QSUB_CMD="${QSUB_COMMON} -o $1.log -e $1.log -N $1"
elif [ "${QUEUE_TYPE}" == "LSF" ]; then
QSUB_CMD="${QSUB_COMMON} -o $1.log -e $1.log -J $1"
elif [ "${QUEUE_TYPE}" == "SLURM" ]; then
QSUB_CMD="${QSUB_COMMON} --output $1.log --error $1.log --job-name $1"
fi
if test "$2" = "" ; then
QSUB_CMD=${QSUB_CMD}
else
if [ "${QUEUE_TYPE}" == "SGE" -o "${QUEUE_TYPE}" == "UGE" ]; then
QSUB_CMD="${QSUB_CMD} -t $2:$3"
elif [ "${QUEUE_TYPE}" == "LSF" ]; then
QSUB_CMD="${QSUB_CMD}[$2-$3]"
elif [ "${QUEUE_TYPE}" == "SLURM" ]; then
QSUB_CMD="${QSUB_CMD} --array $2-$3"
fi
fi
echo ${QSUB_CMD}
}
submit_calcAveDist_ordering() {
EXEC_CMD="perl ${PL_SITE_BY_SITE}"
EXEC_CMD=${EXEC_CMD}" -g ${PHASEFILE} "
EXEC_CMD=${EXEC_CMD}" -d ${ORDER_DIR_LIST} "
EXEC_CMD=${EXEC_CMD}" -l ${ORDER_STRAIN_LIST} "
EXEC_CMD=${EXEC_CMD}" -s ${HAP_LIST_OUTDISP} "
EXEC_CMD=${EXEC_CMD}" -n $1"
if [ "${MISSING_POS_IND_FILE}" != "" ]; then
EXEC_CMD=${EXEC_CMD}" -m ${MISSING_POS_IND_FILE}"
fi
if [ "${CONSTRAINT_FILE}" != "" ]; then
EXEC_CMD=${EXEC_CMD}" -c ${CONSTRAINT_FILE}"
fi
TMP_SH="${STAMP}_n$1_job.sh"
echo "#!/bin/bash" > ${TMP_SH}
echo ${EXEC_CMD} >> ${TMP_SH}
chmod 755 ${TMP_SH}
CMD=`returnQSUB_CMD ${STAMP}`
CMD="${CMD} ./${TMP_SH}"
echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Execution error: ${CMD} (step${STEP})"
fi
}
wait_until_finish() {
while :
do
QSTAT_CMD="squeue -u ${USER} -o \"%.32j\""
END_CHECK=`${QSTAT_CMD} | grep -e $1 | wc -l`
if [ "${END_CHECK}" -eq 0 ]; then
break
fi
echo "Waiting for ${END_CHECK} jobs to complete. Sleeping for 10 seconds."
for w in {1..10}; do
sleep 1
echo -n "$w "
done
echo ""
done
}
submit_msort_each_ordering() {
i_dir=0
while [ "$i_dir" -lt ${#arr_dirs_for_msort[@]} ]; do
date +%Y%m%d_%T
ARRAY_S=1
ARRAY_E=9
CMD=`returnQSUB_CMD ${STAMP} ${ARRAY_S} ${ARRAY_E}`
CMD=${CMD}" ${PL_MSORT_EACH_ORDERING} -d ${arr_dirs_for_msort[$i_dir]} -g ${PHASEFILE} "
echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Execution error: ${CMD} (step${STEP}) "
fi
#
# update the array by removing the submitted dir
#
unset arr_dirs_for_msort[$i_dir]
arr_dirs_for_msort=(${arr_dirs_for_msort[@]})
done
# this loop automatically ends after submitting msort jobs for the decompressed dirs
}
get_stamp() {
DATE_N=`date +%N`
TIME_DIGIT=`echo "$(date +%H%S)$(printf '%02d' $(expr $DATE_N / 10000000))"` # hour(2)sec(2)milisec(2)
#if ls "s$1_${TIME_DIGIT}"* &> /dev/null; then
while ls "s$1_${TIME_DIGIT}"* &> /dev/null
do
sleep 1
DATE_N=`date +%N`
TIME_DIGIT=`echo "$(date +%H%S)$(printf '%02d' $(expr $DATE_N / 10000000))"` # hour(2)sec(2)milisec(2)
done
#fi
STAMP="s$1_${TIME_DIGIT}"
}
disp_punctuate() {
echo "*************** STEP$1, log=$2.log ****************************** "
date +%Y%m%d_%T
}
################################################################################################################
#
# args
#
SEED=1
TYPE_NUM_ORDERING=10 # 20 in total (forward & reverse)
# 9 parallelization for each ordering in the postprocessing
VERBOSE=FALSE
CONTRAST_MAX=-9999
MAX_PARALLEL_DECOMPRESS=20
MISSING_POS_IND_FILE=""
CONSTRAINT_FILE=""
OUTPUT_REPRESENTATIVES=FALSE
while getopts g:t:s:l:o:n:m:c:xv OPTION
do
case $OPTION in
g) if [ ! -z "${OPTARG}" ];then PHASEFILE=${OPTARG} ;else usage ;fi
;;
l) if [ ! -z "${OPTARG}" ];then
HAP_LIST=${OPTARG}
HAP_LIST_OUTDISP=${OPTARG}
else
usage
fi
;;
o) if [ ! -z "${OPTARG}" ];then HAP_LIST_OUTDISP=${OPTARG} ;else usage ;fi
;;
t) if [ ! -z "${OPTARG}" ];then TYPE_NUM_ORDERING=${OPTARG} ;else usage ;fi
;;
s) if [ ! -z "${OPTARG}" ];then SEED=${OPTARG} ;else usage ;fi
;;
n) if [ ! -z "${OPTARG}" ];then MAX_PARALLEL_DECOMPRESS=${OPTARG} ;else usage ;fi
;;
m) if [ ! -z "${OPTARG}" ];then MISSING_POS_IND_FILE=${OPTARG} ;else usage ;fi
;;
c) if [ ! -z "${OPTARG}" ];then CONSTRAINT_FILE=${OPTARG} ;else usage ;fi
;;
x) OUTPUT_REPRESENTATIVES=TRUE
;;
v) VERBOSE=TRUE
;;
\?) usage ;;
esac
done
#
# output files (for error check)
#
# EACH_DIR
OUTF_SITE_DISTSCORE=site_distScore.txt
# COMBINED_RES_DIR
OUTF_SITE_STATS=results_siteStats.txt.gz
OUTF_SUMMARY_POS=results_siteStats_summary.pos.txt
OUTF_SUMMARY_SITE_MINUS_AVERAGE=sum_site_minus_average.summary.txt.gz
OUTF_SUMMARY_RANGE=sum_site_minus_average.summary.range.txt
PNG_HIST=results_siteStats_hist.png
PNG_ALONG_SEQ=results_siteStats_along_seq.png
#
# check env
#
if [ "${QUEUE_TYPE}" == "SGE" -o "${QUEUE_TYPE}" == "UGE" -o "${QUEUE_TYPE}" == "SLURM" ]; then
CHECK=`which qsub`
if [ "${CHECK}" == "" ]; then
echo_fail "Error: qsub is not available"
fi
elif [ "${QUEUE_TYPE}" == "LSF" ]; then
CHECK=`which bsub`
if [ "${CHECK}" == "" ]; then
echo_fail "Error: bsub is not available"
fi
elif [ "${QUEUE_TYPE}" == "SLURM" ]; then
CHECK=`which srun`
if [ "${CHECK}" == "" ]; then
echo_fail "Error: srun is not available"
fi
fi
if [ ! -d "${LOG_DIR}" ]; then
echo_fail "Error: ${LOG_DIR} doesn't exist. Please execute setup.sh first."
fi
if [ ! -d "${LIB_DIR}" ]; then
echo_fail "Error: ${LIB_DIR} doesn't exist. Please execute setup.sh first."
fi
CHECK=`which R`
if [ "${CHECK}" == "" ]; then
echo_fail "Error: R is not installed in PATH"
fi
for aa in ${arr_executable_files[@]}
do
if [ ! -x "${aa}" ]; then
echo_fail "Environment error: ${aa} doesn't exist or is not executable. Please execute setup.sh first."
fi
done
for aa in ${arr_R_files[@]}
do
if [ ! -f "${aa}" ]; then
echo_fail "Environment error: ${aa} doesn't exist"
fi
done
#
# check args
#
if [ $# -lt 2 ] ; then
usage
fi
if [ ! -f "${PHASEFILE}" ]; then
echo_fail "Error: ${PHASEFILE} doesn't exist"
fi
WC_UQ_HAP_LEN=`${PL_CHECK_LINE_LEN} -f ${PHASEFILE} | tail -n +5 | uniq | wc -l`
if [ "${WC_UQ_HAP_LEN}" -gt 1 ]; then
echo_fail "Error: haplotype sequences with different length are found in ${PHASEFILE}"
fi
NUM_IND=`head -2 ${PHASEFILE} | tail -1`
NUM_HAP_IN_PHASEFILE=`wc -l ${PHASEFILE} | awk '{print $1}'`
let NUM_HAP_IN_PHASEFILE=${NUM_HAP_IN_PHASEFILE}-5
if [ ! -f "${HAP_LIST}" ]; then
echo_fail "Error: ${HAP_LIST} doesn't exist"
fi
if [ "${MISSING_POS_IND_FILE}" != "" ]; then
if [ ! -f "${MISSING_POS_IND_FILE}" ]; then
echo_fail "Error: ${MISSING_POS_IND_FILE} doesn't exist"
fi
MAX_MISSING=`awk '{print $1}' ${MISSING_POS_IND_FILE} | uniq -c |sort -n -r |head -1 | awk '{print $1}'`
if [ "${MAX_MISSING}" -ge "${NUM_IND}" ]; then
echo_fail "Error: too many missng data, with maximum=${MAX_MISSING} "
fi
fi
#
# check ${HAP_LIST}
#
CHECK_CR=`head -1 "${HAP_LIST}" | od -c | grep "\r"`
if [ "${CHECK_CR}" != "" ]; then
perl -i -pe 's/\r//g' ${HAP_LIST}
fi
CHECK_PIPE=`cat "${HAP_LIST}" | grep '|'`
if [ "${CHECK_PIPE}" != "" ]; then
perl -i -pe 's/\|/_/g' ${HAP_LIST}
fi
CHECK_REDIRECT=`cat "${HAP_LIST}" | grep '>'`
if [ "${CHECK_REDIRECT}" != "" ]; then
perl -i -pe 's/>//g' ${HAP_LIST}
fi
WC_HAP_LIST=`wc -l ${HAP_LIST} | awk '{print $1}'`
if [ "${WC_HAP_LIST}" -ne "${NUM_IND}" ]; then
echo_fail "Error: The number of rows of ${HAP_LIST} must be ${NUM_IND}, but ${WC_HAP_LIST}"
fi
if [ "${WC_HAP_LIST}" -ne "${NUM_HAP_IN_PHASEFILE}" ]; then
echo_fail "Error: The number of haplotypes in the phasefile is ${NUM_HAP_IN_PHASEFILE}, but the number of lines in ${HAP_LIST} is ${WC_HAP_LIST}"
fi
#
# check ${HAP_LIST_OUTDISP}
#
if [ "${HAP_LIST}" != "${HAP_LIST_OUTDISP}" ]; then
CHECK_CR=`head -1 "${HAP_LIST_OUTDISP}" | od -c | grep "\r"`
if [ "${CHECK_CR}" != "" ]; then
perl -i -pe 's/\r//g' ${HAP_LIST_OUTDISP}
fi
CHECK_PIPE=`cat "${HAP_LIST_OUTDISP}" | grep '|'`
if [ "${CHECK_PIPE}" != "" ]; then
perl -i -pe 's/\|/_/g' ${HAP_LIST_OUTDISP}
fi
WC_HAP_LISTDISP=`wc -l ${HAP_LIST_OUTDISP} | awk '{print $1}'`
if [ "${WC_HAP_LISTDISP}" -ne "${NUM_IND}" ]; then
echo_fail "Error: The number of rows of ${HAP_LIST_OUTDISP} must be ${NUM_IND}, but ${WC_HAP_LISTDISP}"
fi
if [ ! -s "${HAP_LIST_OUTDISP}.names" ]; then
awk '{print $1}' ${HAP_LIST} | sort > ${HAP_LIST}.names
awk '{print $1}' ${HAP_LIST_OUTDISP} | sort > ${HAP_LIST_OUTDISP}.names
DIFF=`diff ${HAP_LIST}.names ${HAP_LIST_OUTDISP}.names`
if [ "${DIFF}" != "" ]; then
echo_fail "Error: difference of names between ${HAP_LIST} and ${HAP_LIST_OUTDISP}: ${DIFF}"
fi
fi
fi
#
# check ${MISSING_POS_IND_FILE}
#
if [ "${MISSING_POS_IND_FILE}" != "" ]; then
CHECK_CR=`head -1 "${MISSING_POS_IND_FILE}" | od -c | grep "\r"`
if [ "${CHECK_CR}" != "" ]; then
perl -i -pe 's/\r//g' ${MISSING_POS_IND_FILE}
fi
if [ ! -s "${MISSING_POS_IND_FILE}.names" ]; then
awk '{print $2}' ${MISSING_POS_IND_FILE} | sort -u > ${MISSING_POS_IND_FILE}.names
if [ ! -s "${HAP_LIST}.names" ]; then
awk '{print $1}' ${HAP_LIST} | sort > ${HAP_LIST}.names
fi
DIFF=`comm -23 ${MISSING_POS_IND_FILE}.names ${HAP_LIST}.names`
if [ "${DIFF}" != "" ]; then
echo_fail "Error: some strain names in ${MISSING_POS_IND_FILE} are not found in ${HAP_LIST}"
fi
fi
fi
echo "All checks passed, preparing for run."
#
# prepare
#
OUT_PREFIX_BASE=`echo ${PHASEFILE} | perl -pe 's/^.*\///g' | perl -pe "s/\.hap//g"`
TGZ_ORDER_PAINTINGS=${OUT_PREFIX_BASE}_orderedS${SEED}_both_paintings.tgz
# output files of STEP2
ORDER_HAP_LIST=${OUT_PREFIX_BASE}_orderedS${SEED}_hap.list
ORDER_DIR_LIST=${OUT_PREFIX_BASE}_orderedS${SEED}_rnd_1_${TYPE_NUM_ORDERING}_dirs.list
ORDER_STRAIN_LIST=${OUT_PREFIX_BASE}_orderedS${SEED}_rnd_1_${TYPE_NUM_ORDERING}_dirs_strainOrder.list
cwd=`dirname $0`
cd $cwd
perl -i -pe 's/\r//g' ${PHASEFILE}
perl -i -pe 's/ $//g' ${PHASEFILE}
################################################################################################################
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# create (uniform) recombination map
# estimation of Ne
# according to http://paintmychromosomes.com/
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
STEP=1
get_stamp ${STEP}
#arr_STAMP=("${arr_STAMP[@]}" "${STAMP}")
disp_punctuate ${STEP} ${STAMP}
NUM_IND=`head -2 ${PHASEFILE} | tail -1 | perl -pe 's/\n//g'`
OUT_DIR_linked1_est=${OUT_PREFIX_BASE}_linked_out1_respartsEM
if [ ! -d "${OUT_DIR_linked1_est}" ]; then
mkdir ${OUT_DIR_linked1_est}
fi
#
# (uniform) recombination map
#
RECOMB_FNANE=${OUT_PREFIX_BASE}_linked.rec
if [ -s "${RECOMB_FNANE}" ]; then
echo "${RECOMB_FNANE} already exists. Skipped."
else
perl ${PL_MAKE_RECMAP} ${PHASEFILE} ${RECOMB_FNANE}
fi
#
# EM inference of Ne (recombination rate) on a subset of data
#
globalparams=""
N_e=""
N_e_FNAME=${OUT_PREFIX_BASE}_linked.neest
if [ -s "${N_e_FNAME}" ]; then
echo "${N_e_FNAME} already exists. Skipped."
else
#
# check format of hap file
#
CMD="${EXE_PAINT} -a 1 1 -j -g $PHASEFILE -r $RECOMB_FNANE -o ${OUT_DIR_linked1_est}/formatcheck > /dev/null 2>&1 &"
echo ${CMD}
eval ${CMD}
PID=$!
if [ $? -ne 0 ]; then
echo_fail "Error: format of $PHASEFILE is wrong. "
else
kill ${PID}
wait ${PID} > /dev/null 2>&1
if ls ${OUT_DIR_linked1_est}/formatcheck* &> /dev/null; then
/bin/rm -f ${OUT_DIR_linked1_est}/formatcheck*
fi
fi
#
# start
#
INCREMENT=1
if [ "${NUM_IND}" -gt 30 ]; then
INCREMENT=`expr $NUM_IND / 30`
let INCREMENT=${INCREMENT}+1
fi
for ind in `seq 1 ${INCREMENT} ${NUM_IND}`
do
out_prefix_ind=${OUT_PREFIX_BASE}_${ind}
EXEC_CMD="${EXE_PAINT} -i ${NUM_EM} -in -n 1 -a $ind $ind -j -g $PHASEFILE -r $RECOMB_FNANE -o ${OUT_DIR_linked1_est}/${out_prefix_ind}"
TMP_SH="${STAMP}_ind${ind}_job.sh"
echo "#!/bin/bash" > ${TMP_SH}
echo ${EXEC_CMD} >> ${TMP_SH}
chmod 755 ${TMP_SH}
CMD=`returnQSUB_CMD ${STAMP}`
CMD="${CMD} ./${TMP_SH}"
echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Execution error: ${CMD} (step${STEP}_1) "
fi
done
echo "Done with batch job submission."
OUT_DIR=${OUT_DIR_linked1_est}
echo "Waiting for jobs to complete."
wait_until_finish "${STAMP}"
# remove unnecessary files
echo "Removing temporary files."
ls ${OUT_DIR_linked1_est}/${OUT_PREFIX_BASE}*.out | grep -v EMprobs | xargs rm -v
ls ${OUT_DIR_linked1_est}/${OUT_PREFIX_BASE}*.copyprobsperlocus.out.gz | xargs rm -v
# summarize *.EMprobs.out files and estimate Ne
echo "Checking for unconverged files."
let WC_CONVERGED=${NUM_EM}+2
for aa in `wc -l ${OUT_DIR_linked1_est}/${OUT_PREFIX_BASE}*.EMprobs.out | grep -v " ${WC_CONVERGED} " | grep -v total | awk '{print $2}'`
do
if [ -f ${aa} ]; then
/bin/mv ${aa} ${aa}.notconverged
fi
done
CMD="${PL_ESTIMATE_Ne} -o ${N_e_FNAME} ${OUT_DIR_linked1_est}/${OUT_PREFIX_BASE}*.EMprobs.out "
echo "executing ${PL_ESTIMATE_Ne} -o ${N_e_FNAME} ${OUT_DIR_linked1_est}/${OUT_PREFIX_BASE}*.EMprobs.out ... "
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Execution error: ${CMD} (step${STEP}_2) "
fi
fi
globalparams=`cat $N_e_FNAME` # $N_e_FNAME contains the commands to tell ChromoPainter about both Ne and global mutation rate, e.g. "-n 10000 -M 0.01".
N_e=`cat $N_e_FNAME | awk '{print $2}' `
if [ "${globalparams}" == "" ]; then
echo_fail "Error (step${STEP}): global params infered by EM are empty"
fi
move_log_files "${STAMP}"
echo "Done with ${STAMP}."
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# prepare ordered *.hap files
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
STEP=2
get_stamp ${STEP}
#arr_STAMP=("${arr_STAMP[@]}" "${STAMP}")
disp_punctuate ${STEP} ${STAMP}
arr_s2_target_ordering=()
#
# check unfinished directories
#
i_ordering=1
while [ "${i_ordering}" -le "${TYPE_NUM_ORDERING}" ]
do
echo "checking ordering (forward and reverse) ${i_ordering} ..."
EACH_DIR_PREFIX=$(printf %s_orderedS%s_rnd%02d ${OUT_PREFIX_BASE} ${SEED} ${i_ordering})
FINISHED_FLAG=FALSE
#
# whether preparation of hap files (STEP2) finished or not
#
if ls ${EACH_DIR_PREFIX}_forward/*.hap &> /dev/null; then
CHECK=`ls ${EACH_DIR_PREFIX}_???????/*.hap | wc -l`
let CHECK=${CHECK}+2
let CORRECT=${NUM_IND}+${NUM_IND}
if [ "${CHECK}" == "${CORRECT}" ]; then
FINISHED_FLAG=TRUE
fi
#
# whether painting (STEP3) finished or not
#
elif ls ${EACH_DIR_PREFIX}_forward/*.copyprobsperlocus.out.gz &> /dev/null; then
CHECK=`ls ${EACH_DIR_PREFIX}_???????/*.copyprobsperlocus.out.gz | wc -l`
let CHECK=${CHECK}+2
let CORRECT=${NUM_IND}+${NUM_IND}
if [ "${CHECK}" == "${CORRECT}" ]; then
FINISHED_FLAG=TRUE
fi
#
# whether ${GZ_CAT_COPYPROB_EACH_DIR}.?? (STEP4) exist or not
#
elif ls ${EACH_DIR_PREFIX}_forward/${GZ_CAT_COPYPROB_EACH_DIR}.?? &> /dev/null; then
CHECK=`ls ${EACH_DIR_PREFIX}_???????/${GZ_CAT_COPYPROB_EACH_DIR}.?? | wc -l`
let CORRECT=${NUM_SPLITN}+${NUM_SPLITN}
if [ "${CHECK}" == "${CORRECT}" ]; then
FINISHED_FLAG=TRUE
fi
#
# incomplete decompressing (STEP4)
#
elif ls ${EACH_DIR_PREFIX}_forward/*.copyprobsperlocus.out_?? &> /dev/null; then
CHECK=`ls ${EACH_DIR_PREFIX}_???????/*.copyprobsperlocus.out_?? | wc -l`
let CORRECT=${NUM_IND}-1
CORRECT=`expr ${CORRECT} \* ${NUM_SPLITN}`
let CORRECT=${CORRECT}+${CORRECT}
if [ "${CHECK}" == "${CORRECT}" ]; then
FINISHED_FLAG=TRUE
fi
for aa in `ls ${EACH_DIR_PREFIX}_???????/*.copyprobsperlocus.out_??`
do
if [ ! -s "${aa}" ]; then
FINISHED_FLAG=FALSE
break
fi
done
fi
#
# store unfinished orderings
#
if [ "${FINISHED_FLAG}" == "FALSE" ]; then
arr_s2_target_ordering+=(${i_ordering})
fi
let i_ordering=${i_ordering}+1
done
#
# execute
#
for i_s2_target_ordering in ${arr_s2_target_ordering[@]}
do
#
# prepare CMD
#
CMD=""
ARRAY_S=1
ARRAY_E=`wc -l ${HAP_LIST} | awk '{print $1}'`
# # arrayjob for i_recipient (can be slower if the num. of available cores is limited)
## CMD=`returnQSUB_CMD ${STAMP} ${ARRAY_S} ${ARRAY_E}`
# CMD=${CMD}" ${SH_RANDOMIZE}"
# CMD=${CMD}" -h ${PHASEFILE}"
# CMD=${CMD}" -p ${OUT_PREFIX_BASE}"
# CMD=${CMD}" -l ${HAP_LIST}"
# CMD=${CMD}" -o ${HAP_LIST_OUTDISP}"
# CMD=${CMD}" -t ${i_s2_target_ordering}"
# CMD=${CMD}" -s ${SEED}"
# qsub for each_ordering
QSUB_FILE=${STAMP}_${OUT_PREFIX_BASE}_orderedS${SEED}_${i_s2_target_ordering}.sh
/bin/cat > ${QSUB_FILE} << EOF
#! /bin/bash
#$ -S /bin/bash
EOF
for i_recipient in `seq ${ARRAY_S} ${ARRAY_E}`
do
/bin/cat >> ${QSUB_FILE} << EOF
${SH_RANDOMIZE} \
-h ${PHASEFILE} \
-p ${OUT_PREFIX_BASE} \
-l ${HAP_LIST} \
-o ${HAP_LIST_OUTDISP} \
-t ${i_s2_target_ordering} \
-i ${i_recipient} \
-s ${SEED}
EOF
done
chmod 755 ${QSUB_FILE}
CMD=`returnQSUB_CMD ${STAMP} `
CMD=${CMD}" ./${QSUB_FILE}"
#
# submit
#
echo ${CMD}
QSUB_MSG=`${CMD}`
if [ $? -ne 0 ]; then
echo_fail "Execution error: ${CMD} (step${STEP}) "
fi
done
wait_until_finish "${STAMP}"
#
# create ${ORDER_HAP_LIST} as a preparation for the next step (painting as arrayjobs)
#
echo "listing up all .hap files to be processed into ${ORDER_HAP_LIST} ..."
/bin/cat /dev/null > ${ORDER_HAP_LIST}
i_ordering=1
while [ "${i_ordering}" -le "${TYPE_NUM_ORDERING}" ]
do
EACH_DIR_PREFIX=$(printf %s_orderedS%s_rnd%02d ${OUT_PREFIX_BASE} ${SEED} ${i_ordering})
if ls ${EACH_DIR_PREFIX}_*/*.hap &> /dev/null; then
CMD="ls ${EACH_DIR_PREFIX}_*/*.hap >> ${ORDER_HAP_LIST}"
#echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Error: ${CMD} "
fi
fi
let i_ordering=${i_ordering}+1
done
wc -l ${ORDER_HAP_LIST}
#
# two list files
#
if [ ! -s "${ORDER_DIR_LIST}" ]; then
CMD="find ./ -maxdepth 1 -type d -name ${OUT_PREFIX_BASE}_orderedS${SEED}_rnd\* | grep -v results | perl -pe 's/^\.\///g' | sort > ${ORDER_DIR_LIST}"
#echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Error: ${ORDER_DIR_LIST} "
fi
echo "${ORDER_DIR_LIST} was created"
fi
if [ ! -s "${ORDER_STRAIN_LIST}" ]; then
CMD="/bin/cat ${ORDER_DIR_LIST} | perl -pe 's/\n/.strainOrder\n/g' > ${ORDER_STRAIN_LIST}"
#echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Error: ${ORDER_STRAIN_LIST} "
fi
echo "${ORDER_STRAIN_LIST} was created"
fi
#
# cleaning tmp files
#
if ls ${STAMP}_${OUT_PREFIX_BASE}_orderedS${SEED}_*.sh &> /dev/null; then
CMD="/bin/rm -f ${STAMP}_${OUT_PREFIX_BASE}_orderedS${SEED}_*.sh"
echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Error: ${CMD} "
fi
fi
if [ -f "${HAP_LIST}.names" ]; then
CMD="/bin/rm -f ${HAP_LIST}.names"
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Error: ${CMD} "
fi
fi
if [ -f "${HAP_LIST_OUTDISP}.names" ]; then
CMD="/bin/rm -f ${HAP_LIST_OUTDISP}.names"
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Error: ${CMD} "
fi
fi
move_log_files "${STAMP}"
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# execute chromopainter for each ordered recipient haplotype
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
STEP=3
get_stamp ${STEP}
disp_punctuate ${STEP} ${STAMP}
TARGET_HAP_FNANE="target_hap.list"
while read EACH_DIR
do
#
# prepare $TARGET_HAP_LIST, $NUM_TARGET_HAP
#
NUM_TARGET_HAP=0
TARGET_HAP_LIST="${EACH_DIR}/${TARGET_HAP_FNANE}"
/bin/cat /dev/null > ${TARGET_HAP_LIST}
echo "preparing ${TARGET_HAP_LIST} ... "
#
# skip this ordered directory if there is already all ${GZ_CAT_COPYPROB_EACH_DIR}.??
#
SKIP_FLAG=0
if ls ${EACH_DIR}/${GZ_CAT_COPYPROB_EACH_DIR}.?? &> /dev/null; then
CHECK=`ls ${EACH_DIR}/${GZ_CAT_COPYPROB_EACH_DIR}.?? | wc -l`
if [ "${CHECK}" == "${NUM_SPLITN}" ]; then
SKIP_FLAG=1
fi
fi
if [ "${SKIP_FLAG}" -eq 1 ]; then
echo "painting in ${EACH_DIR} is skipped because there are already ${NUM_SPLITN} ${GZ_CAT_COPYPROB_EACH_DIR}. files"
else
for EACH_HAP in `grep ${EACH_DIR} ${ORDER_HAP_LIST}`
do
EACH_COPYPROB_GZ=`echo ${EACH_HAP} | perl -pe 's/\.hap$/.copyprobsperlocus.out.gz/g'`
target_flag=0
if [ ! -s "${EACH_COPYPROB_GZ}" ]; then
target_flag=1
else
CHECK_HEAD=`gzip -dc ${EACH_COPYPROB_GZ} | head | wc -l`
if [ $? -ne 0 -o "${CHECK_HEAD}" -eq 0 ]; then
target_flag=1
/bin/rm -f ${EACH_COPYPROB_GZ}
echo "incomplete ${EACH_COPYPROB_GZ} was removed"
fi
fi
# execute painting of unfinished hap files in this ordered directory
if [ "${target_flag}" -eq 1 ]; then
echo ${EACH_HAP} >> ${TARGET_HAP_LIST}
let NUM_TARGET_HAP=${NUM_TARGET_HAP}+1
else
echo "${EACH_COPYPROB_GZ} already exists. ${EACH_HAP} is skipped and removed."
if [ -f "${EACH_HAP}" ]; then
/bin/rm -f ${EACH_HAP}
fi
fi
done
#
# execute paining of the target hap files
#
if [ "${NUM_TARGET_HAP}" -eq 0 ]; then
echo "${EACH_DIR} was skipped because there is no hap file to be painted."
else
ARRAY_S=1
ARRAY_E=${NUM_TARGET_HAP}
CMD=`returnQSUB_CMD ${STAMP} ${ARRAY_S} ${ARRAY_E}`
#CMD=${CMD}" -t 1:${NUM_TARGET_HAP} "
CMD=${CMD}" ${SH_PAINT_QSUB}"
CMD=${CMD}" -r ${RECOMB_FNANE}"
CMD=${CMD}" -n ${N_e_FNAME}"
CMD=${CMD}" -l ${TARGET_HAP_LIST}"
echo ${CMD}
eval ${CMD}
if [ $? -ne 0 ]; then
echo_fail "Execution error: ${CMD} (step${STEP}) "
fi
#QSUB_ID=`echo ${QSUB_MSG} | perl -pe 's/ \(.*$//g' | perl -pe 's/^.* //g' | perl -pe 's/\..*$//g'`
fi
fi
done < ${ORDER_DIR_LIST}
wait_until_finish "${STAMP}"
echo "checking whether there is any incomplete output file (.copyprobsperlocus.out.gz) of the step${STEP} ..."
i_failed=0
while read EACH_DIR
do
echo "${EACH_DIR}"
i_HAP=0
TARGET_HAP_LIST="${EACH_DIR}/${TARGET_HAP_FNANE}"
while read EACH_HAP
do
let i_HAP=${i_HAP}+1
EACH_COPYPROB_GZ=`echo ${EACH_HAP} | perl -pe 's/\.hap/.copyprobsperlocus.out.gz/g'`
if [ -f "${EACH_COPYPROB_GZ}" ]; then
CHECK_HEAD=`gzip -dc ${EACH_COPYPROB_GZ} | head | wc -l`
if [ $? -ne 0 -o "${CHECK_HEAD}" -eq 0 ]; then
echo "painting of ${EACH_HAP} failed, because ${EACH_COPYPROB_GZ} is an incomplete file"
let i_failed=${i_failed}+1
/bin/rm -f ${EACH_COPYPROB_GZ}
echo "incomplete ${EACH_COPYPROB_GZ} was removed"
fi
else
sleep 10 # just in case of a problem of timing to write files in your file system
if [ ! -f "${EACH_COPYPROB_GZ}" ]; then
echo "painting of ${EACH_HAP} failed, because there is no ${EACH_COPYPROB_GZ}"
let i_failed=${i_failed}+1
fi
fi
done < "${TARGET_HAP_LIST}"
done < ${ORDER_DIR_LIST}
if [ "${i_failed}" -gt 0 ]; then
echo_fail "There are ${i_failed} failed jobs. Please execute this program again (already finished jobs will be skipped)."
fi
move_log_files "${STAMP}"
################################################################################################################
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Formatting output files of ChromoPainter
#
# for each ordering,
# split
# msort to ${GZ_CAT_COPYPROB_EACH_DIR}.??
#
# it can require a large temporary disk in each ordering
#
#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
STEP=4
get_stamp ${STEP}
#arr_STAMP=("${arr_STAMP[@]}" "${STAMP}")
disp_punctuate ${STEP} ${STAMP}
TARGET_GZ_FNANE="target_gz.list"
declare -a arr_dirs_for_msort