3a_ImputeScriptMaker.sh

#!/bin/bash 


## Overview:
## ==================

## This script will:
	# 1) Create the Bash scripts used to execute Imputation jobs (autosomal and the X chromosome) on a system
	# 2) Submit the Bash scripts to the HPC queue at the user's request
	
## ==========================================================================================


# Splash Screen
# --------------
	source .TitleSplash.txt
	printf "$Logo"

# Source from .config files (Program options via Settings.conf & Program execs via Programs.conf)
# ----------------------------
	source Settings.conf
	
	# Load Odysseys Dependencies -- pick from several methods
	if [ "${OdysseySetup,,}" == "one" ]; then
		echo
		printf "\n\nLoading Odyssey's Singularity Container Image \n\n\n"
		source ./Configuration/Setup/Programs-Singularity.conf
	
	elif [ "${OdysseySetup,,}" == "two" ]; then
		echo
		printf "\n\nLoading Odyssey's Manually Configured Dependencies \n\n\n"
	else

		echo
		echo User Input Not Recognized -- Please specify One or Two
		echo Exiting Dependency Loading
		echo
		exit
	fi


# Set Working Directory
# -------------------------------------------------
echo
echo Changing to Working Directory
echo ----------------------------------------------
echo ${WorkingDir}
echo
echo

	cd ${WorkingDir}


# ======================================================================================================
# ======================================================================================================
#                                       Error Check for Shapeit
# ======================================================================================================
# ======================================================================================================

if [ "${UseShapeit,,}" == "t" ]; then

	# Perform Error Analysis on Phasing Step -- grep looks for .out files containing 'Killed', 'Aborted', 'segmentation', or 'error'
	# -----------------------------
	
	if [ "${PhasingErrorAnalysis,,}" == "t" ]; then
	
		echo
		echo --------------------------------------------------------
		echo Performing Error Analysis on Phasing Jobs:
		echo --------------------------------------------------------
		echo 
		echo
		echo Phasing jobs that should be reviewed are listed:
		echo It may take a while to scan all the .out files
		echo ==============================================
		echo
		find ./2_Phase/${BaseName}/Scripts2Shapeit -maxdepth 1 -type f -print | xargs grep -rli 'Killed\|Aborted\|segmentation\|error' | sort -V
		echo
		echo ==============================================
		echo
	
	# Examine the failed files?
		echo
		echo "The files listed above appeared to have failed." 
		echo "Would you like more details on why they failed (this will print the line that contains the error for each failed file)?"
		echo "(y/n)?"
		echo --------------------------------------------------
		read UserInput1
		echo
		echo
		
		if [ "${UserInput1}" == "y" ]; then
			
			echo
			echo "Outputting more details on failed file/s..."
			echo ===========================================
			echo
			find ./2_Phase/${BaseName}/Scripts2Shapeit -maxdepth 1 -type f -print | xargs grep -ri 'Killed\|Aborted\|segmentation\|error' | sort -V
			echo
			echo ===========================================
		
		else
			if [ "${UserInput1,,}" == "n" ]; then
			
			echo "Alright, will not output more details on failed file/s"
			echo =========================================================
			echo
	
			else
				echo "Input not recognized -- specify either 'y' or 'n' -- exiting Error Analysis"
				echo ================================================================================
				echo
			fi
		fi
		
	# Re-submit the failed scripts
		echo
		echo "Would you like to resubmit the failed scripts?" 
		echo "Script/s will be submitted to an HPS if specified in Settings.conf otherwise will submit via a simple 'sh' command"
		echo "(y/n)?"
		echo --------------------------------------------------
		read UserInput2
		echo
		echo
		
		if [ "${UserInput2,,}" == "y" ]; then
			
			# Specify text document of failed scripts to re-run; manual script re-submission
			echo
			echo "Normally ALL the failed scripts will be re-submitted" 
			echo "However, you can provide a text doc that contains a list of the scripts you would like re-submitted"
			echo "Would you prefer to manually provide this list?"
			echo "Note: The file should contain the full path to the automatically created scripts you want re-submitted"
			echo "Note: Each script should be listed on a new line of the text document"
			echo "(y/n)?"
			echo --------------------------------------------------
			read UserInput3
			echo
			echo
				if [ "${UserInput3,,}" == "y" ]; then
					echo "You Said Yes to Manual Script Submission So Please Provide the Full Path to the Re-Submission Text Doc"
					read UserInput4
					echo "Using Text Doc: ${UserInput4} for manual script submission"
				
				elif [ "${UserInput3}" == "n" ]; then
						echo
				else 
					echo "User Input not recognized -- please specify 'y' or 'n' -- ignoring input"
					
				fi
				
			if [ "${HPS_Submit,,}" == "t" ]; then
	
			
				echo
				echo Re-Submitting Failed Scripts to HPS...
				echo ===========================================
				echo
				# The following line does a lot: 
				# 1) looks in the script directory that also contains output logs 
				# 2) find .out files that contain the words 'Killed', 'Aborted', 'segmentation', or 'error'
				# 3,4) Sorts the .out files and subs .out for .sh to get the script
				# 5) Within .sh should be a manual execution command that starts with '# qsub', grep finds the line and trims the off the '# ' to get the qsub command and saves it to ReSubmitPhaseJobs.txt
					find ./2_Phase/${BaseName}/Scripts2Shapeit -maxdepth 1 -type f -print | xargs grep -rli 'Killed\|Aborted\|segmentation\|error' | sort -V | sed 's/.out/.sh/g' | xargs grep -r 'qsub' | sed 's/.*# //' > ReSubmitPhaseJobs.txt
					
					# Manually read in scripts that need to be re-run (comment out previous command if you want to use this manual override				
						#cat ./2_Phase/${BaseName}/Scripts2Resubmit.txt | sort -V | sed 's/.out/.sh/g' | xargs grep -r 'qsub' | sed 's/.*# //' > ReSubmitPhaseJobs.txt
				
				# Remove the errored .out file (otherwise the new .out will be appended to the old and the error will never be reported as fixed)
					find ./2_Phase/${BaseName}/Scripts2Shapeit -maxdepth 1 -type f -print | xargs grep -rli 'Killed\|Aborted\|segmentation\|error' | sort -V | xargs rm -f
			
				# Read the file that contains the scripts that need to be re-submitted and submit then via Bash to the HPS queue
					cat ReSubmitPhaseJobs.txt | bash
				
				# Remove ReSubmitJobs.txt
					rm -f ReSubmitPhaseJobs.txt
			
				echo
				echo ===========================================
				echo
			
			else
				echo
				echo Re-Submitting Failed Scripts to Desktop...
				echo ===========================================
				echo
				# The following line does a lot: 
				# 1) looks in the script directory that also contains output 
				# 2) find .out files that contain the words 'Killed', 'Aborted', 'segmentation', or 'error'
				# 3,4) Sorts the .out files and subs .out for .sh to get the script
				# 5) Within .sh should be a manual execution command that starts with 'time ', grep finds the line and saves it to ReSubmitPhaseJobs.txt
					find ./2_Phase/${BaseName}/Scripts2Shapeit -maxdepth 1 -type f -print | xargs grep -rli 'Killed\|Aborted\|segmentation\|error' | sort -V | sed 's/.out/.sh/g' | xargs grep -r 'time ' > ReSubmitPhaseJobs.txt
			
				# Remove the errored .out file (otherwise the new .out will be appended to the old and the error will never be reported as fixed)
					find ./2_Phase/${BaseName}/Scripts2Shapeit -maxdepth 1 -type f -print | xargs grep -rli 'Killed\|Aborted\|segmentation\|error' | sort -V | xargs rm -f
			
				# Read the file that contains the scripts that need to be re-submitted and submit then via sh to the Linux workstation
					cat ReSubmitPhaseJobs.txt | bash
				
				# Remove ReSubmitJobs.txt
					rm -f ReSubmitPhaseJobs.txt
			
				echo
				echo ===========================================
				echo
			fi
				
				
		
		else
			if [ "${UserInput2,,}" == "n" ]; then
			
			echo "Alright, will not Re-Submit Failed Script/s"
			echo ==============================================
			echo
			echo
	
			else
				echo "Input Not Recognized -- Specify Either 'y' or 'n' -- Exiting Re-Submission"
				echo ==============================================================================
				echo
				echo
			fi
		fi
	fi
fi

# ======================================================================================================
# ======================================================================================================
#                                    Imputation Script Creation
# ======================================================================================================
# ======================================================================================================


# Creates the Impute directory and also Lustre Stripes it to accomidate for large file folders (prevents the file folder from completely filling up a drive)
	
	printf "\nCreating Imputation Project Folder within Impute Directory \n\n\n"
		mkdir -p ./3_Impute/${BaseName}
	
	# Use Lustre Stripping?
		if [ "${LustreStrip,,}" == "t" ]; then
			lfs setstripe -c 5 ./3_Impute/${BaseName}
		fi

	mkdir -p ./3_Impute/${BaseName}/Scripts2Impute
	mkdir -p ./3_Impute/${BaseName}/RawImputation


# ---------------------------------------------
# Formatting the Fam file to an Imputation Sample File
# ---------------------------------------------


	# LEGACY Format Shapeit Sample File for Use with Impute	

	#Get a single sample file from the Phase folder
	#SHAPEIT_SAMPLE_FILE="$(ls ./2_Phase/${BaseName}/*.sample | head -1)"
	
	#echo
	#echo Modifying Sample File: 
	#echo $SHAPEIT_SAMPLE_FILE 
	#echo to be used with Impute4
	#echo -----------------------------------
	#echo
	#awk 'BEGIN{FS=" "}{print $1,$2,$3,$6}' OFS=' ' $SHAPEIT_SAMPLE_FILE > ./3_Impute/${BaseName}/${BaseName}.sample

	#Get a QC2 .fam file from the Target folder and format it for Minimac/Impute
		PLINK_FAM_FILE="$(ls ./1_Target/${BaseName}/*QC2.fam | head -1)"
		
		echo
		echo Modifying Fam File: 
		echo $PLINK_FAM_FILE
		printf "  ...into a Sample File\n"
		echo -----------------------------------
		echo
			# Cutnecessary Columns
				awk 'BEGIN{FS=" "}{print $1,$2,$4,$5}' OFS=' ' $PLINK_FAM_FILE > ./3_Impute/${BaseName}/${BaseName}.sampleTEMP

			# Format the Plink QC2 .fam file for Imputation via Impute
				echo -e "ID_1 ID_2 missing sex\n0 0 0 D" | cat - ./3_Impute/${BaseName}/${BaseName}.sampleTEMP > ./3_Impute/${BaseName}/${BaseName}.sample
			
			# Remove the Temp File
				rm ./3_Impute/${BaseName}/${BaseName}.sampleTEMP


## --------------------------------------------------------------------------------------
## ===========================================
##          Impute Imputation
## ===========================================
## --------------------------------------------------------------------------------------


if [ "${UseImpute,,}" == "t" ]; then

	# ---------------------------------------------
	## Toggle whether to Impute the Autosomes (Chr1-22)
	# ---------------------------------------------
	
	if [ "${ImputeAutosomes,,}" == "t" ]; then 
	
		#Set Chromosome Start and End Parameters
		for chr in `eval echo {$ImputeChrStart..$ImputeChrEnd}`; do
			printf "\nProcessing Chromosome ${chr} Scripts \n"
			echo -----------------------------------
			echo
	
			#Search the reference directory for the chromosome specific reference map, legend, and hap files and create their respective variables on the fly
				echo "Looking in ./Reference For Reference Files "
				echo "Found the following references for Chromosome ${chr}: "
	
				GeneticMap="$(ls ./Reference/ | egrep --ignore-case ".*map.*chr${chr}[^[:digit:]]{1}.*|.*chr${chr}[^[:digit:]]{1}.*map.*")"
				printf "   Genetic Map File: $GeneticMap \n"
				HapFile="$(ls ./Reference/ | egrep --ignore-case ".*chr${chr}[^[:digit:]]{1}.*hap\.gz")"
				printf "   Haplotpe File: $HapFile \n"
				LegendFile="$(ls ./Reference/ | egrep --ignore-case ".*chr${chr}[^[:digit:]]{1}.*legend\.gz")"
				printf "   Legend File: $LegendFile \n\n"	
	
			# Check to see if all reference files + genetic map exist
			if [[ -f ./Reference/${GeneticMap} && -f ./Reference/${HapFile} && -f ./Reference/${LegendFile} ]] ; then
			
				# Create bash files to segment chromosomes by position and create imputation scripts
				echo
				echo All Necessary Reference Files Present for Chr${chr}
				echo Segmenting Chromosome and Creating Scripts
				echo	
	
				# Change to Working Directory
				cd ${WorkingDir}
	
				# Figure out how many chunks there are per chromosome by doing some algebra on the genetic map file
				maxPos=$(gawk '$1!="position" {print $1}' ./Reference/${GeneticMap} | sort -n | tail -n 1);
				nrChunk=$(expr ${maxPos} "/" 5000000);
				nrChunk2=$(expr ${nrChunk} "+" 1);
				start="0";
	
				## Make each chunk an imputation job and setup the script
				# --------------------------------------------------------
	
				for chunk in $(seq 1 $nrChunk2); do
					endchr=$(expr $start "+" 5000000);
					startchr=$(expr $start "+" 1);
	
		
echo "#!/bin/bash

cd ${WorkingDir}

# Impute Manual Command Used to re-run autosomal imputation in case of failure
	# qsub -l nodes=1:ppn=1,vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.out -N IChr${chr}_ck${chunk}_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.sh


# Impute 4 Automatic Command -- Currently enabled to impute the autosomal chromosomes

printf '\n\n'	
echo ========================================
printf 'Impute Chr${chr} Using Impute4\n'
echo ========================================
printf '\n\n'

${Impute4_Exec} \
-g ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr${chr}_Phased.haps.gz \
-s ./3_Impute/${BaseName}/${BaseName}.sample \
-m ./Reference/${GeneticMap} \
-h ./Reference/${HapFile} \
-l ./Reference/${LegendFile} \
-int ${startchr} ${endchr} \
-maf_align -Ne 20000 \
-o ./3_Impute/${BaseName}/RawImputation/Ody4_${BaseName}_Chr${chr}_Chunk${chunk}

# Legacy Impute 2 Automatic Command -- Currently disabled to impute the autosomal chromosomes
	# Remove the hashtag from the Impute2 command below and comment out (include a hastag before) the Impute4 command above to run Impute2 for the autosomal chromosomes

#${Impute2_Exec} \
-known_haps_g ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr${chr}_Phased.haps.gz \
-sample_g ./3_Impute/${BaseName}/${BaseName}.sample \
-m ./Reference/${GeneticMap} \
-h ./Reference/${HapFile} \
-l ./Reference/${LegendFile} \
-int ${startchr} ${endchr} \
-Ne 20000 \
-o ./3_Impute/${BaseName}/RawImputation/Ody4_${BaseName}_Chr${chr}_Chunk${chunk}" > ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.sh


					start=${endchr};
	
	
					# Toggle that will turn script submission on/off
					# -----------------------------------------------
	
					if [ "${ExecuteImputationScripts,,}" == "t" ]; then
		
						if [ "${HPS_Submit,,}" == "t" ]; then
	
							echo
							echo Submitting Impute script to HPC Queue
							echo
							qsub -l nodes=1:ppn=1,vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.out -N IChr${chr}_ck${chunk}_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.sh
						else
			
							echo
							echo Submitting Impute script to Desktop Queue
							echo
							bash ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.sh > ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_Chunk${chunk}_${BaseName}_I.out 2>&1 &
	
				
						fi	
					fi
				done
		
			else
				echo
				echo All Necessary Reference Files Not Present
				echo Will Not Segment or Create Scripts
				echo
			fi
		done
	fi



	# ---------------------------------------------
	## Toggle whether to Impute the X Chromosome
	# ---------------------------------------------
	
	if [ "${ImputeX,,}" == "t" ]; then
		echo Processing X Chromosome Scripts
		echo -----------------------------------
		
	
		# Search the reference directory for the X chromosome specific reference map, legend, and hap files and create their respective variables on the fly
		
			echo "Looking in ./Reference For Reference Files "
			echo "Found the following references for Chromosome X: "
	
			XGeneticMap="$(ls ./Reference/ | egrep --ignore-case ".*map.*${XChromIdentifier}.*|.*${XChromIdentifier}.*map.*")"
				printf "   Genetic Map: $XGeneticMap \n"
			XHapFile="$(ls ./Reference/ | egrep --ignore-case ".*${XChromIdentifier}.*hap\.gz")"
				printf "   Haplotpe File: $XHapFile \n"
			XLegendFile="$(ls ./Reference/ | egrep --ignore-case ".*${XChromIdentifier}.*legend\.gz")"
				printf "   Legend File: $XLegendFile \n \n"
	
		# Check to see if all reference files + genetic map exist
		if [[ -f ./Reference/${XGeneticMap} && -f ./Reference/${XHapFile} && -f ./Reference/${XLegendFile} ]] ; then
			
	
			# Create bash files to segment chromosomes by position and create imputation scripts
			echo
			echo All Necessary Reference Files Present for ChrX
			echo Segmenting Chromosome and Creating Scripts
			echo
		
		
			## Figure out how many chunks there are on the X Chromosome by doing some algebra on the genetic map file
			#----------------------------------------------------------------------------------------------------------
			maxPos=$(gawk '$1!="position" {print $1}' ./Reference/${XGeneticMap} | sort -n | tail -n 1);
			nrChunk=$(expr ${maxPos} "/" 5000000);
			nrChunk2=$(expr ${nrChunk} "+" 1);
			start="0";
		
			## Make each chunk an imputation job and setup script
			# ----------------------------------------------------
			for chunk in $(seq 1 $nrChunk2); do
				endchr=$(expr $start "+" 5000000);
				startchr=$(expr $start "+" 1);
	
			
echo "#!/bin/bash

cd ${WorkingDir}

# Impute Manual Command Used to re-run X chromosome imputation in case of failure
	# qsub -l nodes=1:ppn=1,vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.out -N IChr23_ck${chunk}_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.sh

# Impute 4 X chromosome Automatic Command -- Currently enabled to impute the X chromosome

printf '\n\n'	
echo ========================================
printf 'Impute ChrX Using Impute4\n'
echo ========================================
printf '\n\n'

${Impute4_Exec} \
-chrX \
-g ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.haps.gz \
-s ./3_Impute/${BaseName}/${BaseName}.sample \
-m ./Reference/${XGeneticMap} \
-h ./Reference/${XHapFile} \
-l ./Reference/${XLegendFile} \
-int ${startchr} ${endchr} \
-maf_align \
-o ./3_Impute/${BaseName}/RawImputation/Ody4_${BaseName}_Chr23_Chunk${chunk}


# Legacy Impute 2 Automatic Command -- Currently disabled to impute the X chromosome
	# Remove the hashtag from the Impute2 command below and comment out (include a hastag before) the Impute4 command above to run Impute2 for the X chromosome

#${Impute2_Exec} \
-chrX \
-known_haps_g ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.haps \
-sample_g ./3_Impute/${BaseName}/${BaseName}.sample \
-m ./Reference/${XGeneticMap} \
-h ./Reference/${XHapFile} \
-l ./Reference/${XLegendFile} \
-int ${startchr} ${endchr} \
-o ./3_Impute/${BaseName}/RawImputation/Ody4_${BaseName}_Chr23_Chunk${chunk}.gen" > ./3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.sh

				start=${endchr};
		
				# Toggle that will turn script submission on/off
				# -----------------------------------------------
				if [ "${ExecuteImputationScripts,,}" == "t" ]; then
	
		
					if [ "${HPS_Submit,,}" == "t" ]; then
	
						echo
						echo Submitting Impute script to HPC Queue
						echo
						qsub -l nodes=1:ppn=1,vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.out -N IChr23_ck${chunk}_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.sh
					elif [ "${HPS_Submit,,}" == "f" ]; then
					
						echo
						echo Submitting Impute script to Desktop Queue
						echo
						bash ./3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.sh > ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr23_Chunk${chunk}_${BaseName}_I.out 2>&1 &
	
					else
					
						echo
						echo User Input Not Recognized -- Please specify T or F
						echo Exiting script submission
						echo
					fi
				elif [ "${ExecuteImputationScripts,,}" == "f" ]; then
				
					echo
					echo Not Submitting Scripts
					echo
				
				else
					echo
					echo User Input Not Recognized -- Please specify T or F
					echo Exiting script submission
					echo
				fi
			done
		else
			echo
			echo All Necessary Reference Files Not Present
			echo Will Not Segment or Create Scripts
			echo
		fi	
	fi
fi



## --------------------------------------------------------------------------------------
## ===========================================
##          Minimac Imputation
## ===========================================
## --------------------------------------------------------------------------------------

if [ "${UseMinimac,,}" == "t" ]; then


	# ---------------------------------------------
	## Toggle whether to Impute the Autosomes (Chr1-22)
	# ---------------------------------------------
	
	if [ "${ImputeAutosomes,,}" == "t" ]; then 
	
		#Set Chromosome Start and End Parameters
		for chr in `eval echo {$ImputeChrStart..$ImputeChrEnd}`; do
			printf "\nProcessing Chromosome ${chr} Scripts \n"
			echo -----------------------------------
				
			#Search the reference directory for the chromosome specific reference map, legend, and hap files and create their respective variables on the fly
				echo "Looking in ./Reference For Minimac .m3vcf Reference Files "
				echo "Found the following references for Chromosome ${chr}: "
	
				MiniRef="$(ls ./Reference/ | egrep --ignore-case "^${chr}[^[:digit:]]{1}.*\.m3vcf\.gz")"
				printf "   $MiniRef \n"

			# Check to see if all reference files + genetic map exist
				if [[ -f ./Reference/${MiniRef} ]] ; then
			
					# Create bash files to segment chromosomes by position and create imputation scripts
						echo
						echo All Necessary Reference Files Present for Chr${chr}
						echo
						echo Creating Scripts
						echo	
			
					# Change to Working Directory
						cd ${WorkingDir}
		
echo "#!/bin/bash

cd ${WorkingDir}

# Minimac Manual Command Used to re-run autosomal imputation in case of failure
	# qsub -l nodes=1:ppn=${ImputeThreads},vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.out -N IChr${chr}_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.sh

# Convert Chr Phased haps to VCF

printf '\n\n'	
echo ========================================
printf 'Convert Chr${chr} Phased .haps to .vcf\n'
echo ========================================
printf '\n\n'

${Shapeit2_Exec} -convert --input-haps ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr${chr}_Phased --output-vcf ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr${chr}_Phased.vcf.gz --output-log ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr${chr}_Phased.vcf.log.temp


# Minimac Command

printf '\n\n'	
echo ========================================
printf 'Impute Chr${chr} Using Minimac\n'
echo ========================================
printf '\n\n'

${Minimac4_Exec} \
--cpus $ImputeThreads \
--allTypedSites --minRatio 0.00001 \
--refHaps ./Reference/${MiniRef} \
--haps ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr${chr}_Phased.vcf.gz \
--prefix ./3_Impute/${BaseName}/RawImputation/Ody4_${BaseName}_Chr${chr}" > ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.sh
	
					# Toggle that will turn script submission on/off
					# -----------------------------------------------
					
					if [ "${ExecuteImputationScripts,,}" == "t" ]; then
					
						if [ "${HPS_Submit,,}" == "t" ]; then
					
							echo
							echo
							echo Submitting Impute script to HPC Queue
							echo
							qsub -l nodes=1:ppn=${ImputeThreads},vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.out -N IChr${chr}_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.sh
						else
					
							echo
							echo Submitting Impute script to Desktop Queue
							echo
							bash ./3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.sh > ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr${chr}_${BaseName}_I.out 2>&1 &
					
					
						fi	
					fi
		
				else
					echo
					echo All Necessary Reference Files Not Present
					echo Will Not Segment or Create Scripts
					echo
				fi
		done
	fi

	# ---------------------------------------------
	## Toggle whether to Impute the X Chromosome
	# ---------------------------------------------
		
	if [ "${ImputeX,,}" == "t" ]; then
		echo
		echo Processing X Chromosome Scripts
		echo -----------------------------------
		
		
		
		#Search the reference directory for the chromosome specific reference map, legend, and hap files and create their respective variables on the fly
			echo "Looking in ./Reference For Minimac .m3vcf Reference Files "
			echo "Found the following references for Chromosome X: "
	
			XMiniRef="$(ls ./Reference/ | egrep --ignore-case "^${XChromIdentifier}[^[:digit:]]{1}.*\.m3vcf\.gz")"
			printf "   Minimac Ref File: $XMiniRef \n"

		# Check to see if all reference files + genetic map exist
		if [[ -f ./Reference/${XMiniRef} ]] ; then
			
			# Create bash files to segment chromosomes by position and create imputation scripts
				echo
				echo All Necessary Reference Files Present for Chr X
				echo Creating Scripts
				echo	
			
			# Change to Working Directory
				cd ${WorkingDir}
			
echo "#!/bin/bash

cd ${WorkingDir}

# Minimac Manual Command Used to re-run X chromosome imputation in case of failure
	# qsub -l nodes=1:ppn=${ImputeThreads},vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.out -N IChr23_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.sh

# Convert Chr Phased haps to VCF


	printf '\n\n'	
	echo ========================================
	printf 'Convert ChrX Phased .haps to .vcf\n'
	echo ========================================
	printf '\n\n'

	${Shapeit2_Exec} -convert --input-haps ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased --output-vcf ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.temp --output-log ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.log.temp

# Format the VCF.gz so that Chr23 is XChromIdentifier
	printf '\n\n'	
	echo ========================================
	printf 'Relabel Chr23 .vcf to X and Gzip\n'
	echo ========================================
	printf '\n\n'
	
	# Get the header # rows from the VCF
		grep -w \"#\" ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.temp > ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf
	
	# For some readon the column header row isn't taken so specifically ask for it	
		grep -w \"CHROM\" ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.temp >> ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf
	
	#Get the rest of the VCF except this time replace 23 with 'X'
		awk '/^[^#]/ { first = \$1; \$1 = \"X\"; print \$0}' OFS='\t' ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.temp >> ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf
		
	# Remove the Temp file
		rm ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.temp

	# Gzip the output 
		${gzip_Exec} ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf


# Minimac Command

	printf '\n\n'	
	echo ========================================
	printf 'Impute ChrX Using Minimac\n'
	echo ========================================
	printf '\n\n'

# Minimac Command
	${Minimac4_Exec} \
	--cpus $ImputeThreads \
	--allTypedSites --minRatio 0.00001 \
	--refHaps ./Reference/${XMiniRef} \
	--haps ./2_Phase/${BaseName}/Ody3_${BaseName}_Chr23_Phased.vcf.gz \
	--prefix ./3_Impute/${BaseName}/RawImputation/Ody4_${BaseName}_Chr23" > ./3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.sh
    
		
			# Toggle that will turn script submission on/off
			# -----------------------------------------------
			if [ "${ExecuteImputationScripts,,}" == "t" ]; then
	
	
				if [ "${HPS_Submit,,}" == "t" ]; then
	
					echo
					echo Submitting Impute script to HPC Queue
					echo
					qsub -l nodes=1:ppn=${ImputeThreads},vmem=${Impute_Memory}gb,walltime=${Impute_Walltime} -M ${Email} -m a -j oe -o ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.out -N IChr23_${BaseName} ./3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.sh
				
				elif [ "${HPS_Submit,,}" == "f" ]; then
				
					echo
					echo Submitting Impute script to Desktop Queue
					echo
					bash ./3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.sh > ${WorkingDir}3_Impute/${BaseName}/Scripts2Impute/Chr23_${BaseName}_I.out 2>&1 &
	
				else
				
					echo
					echo User Input Not Recognized -- Please specify T or F
					echo Exiting script submission
					echo
				fi
			elif [ "${ExecuteImputationScripts,,}" == "f" ]; then
			
				echo
				echo Not Submitting Scripts
				echo
			
			else
				echo
				echo User Input Not Recognized -- Please specify T or F
				echo Exiting Script Submission
				echo
			fi
			
		else
			echo
			echo All Necessary Reference Files Not Present
			echo Will Not Segment or Create Scripts
			echo
		fi	
	fi
fi

# Termination Message
	echo
	echo ============
	echo " Phew Done!"
	echo ============
	echo
	echo