update_build.sh

#!/bin/sh

#A script for updating a binary ped file using one of Will's strand files
#NRR 17th Jan 2012

#V2 13th Feb 2012. Added code to retain only SNPs in the strand file

#Required parameters:
#1. The original bed stem (not including file extension suffix)
#2. The strand file to apply
#3. The new stem for output
#Result: A new bed file (etc) using the new stem

#Required parameters:
#1. The original bed stem (not including file extension suffix)
#2. The strand file to apply
#3. The new stem for output
#Result: A new bed file (etc) using the new stem

#Added by M. Forest to match the plink version we have
PLINK_EXEC=`which plink`

#Unpack the parameters into labelled variables
stem=$1
input_dir=$2
strand_file=$3
outstem=$4
output=$5
remove_multi=$6
echo Input stem is $stem
echo Strand file is $strand_file
echo Output stem is $outstem

#Cut the strand file into a file for flipping strand when necessary
flip_file=$output/$strand_file.flip
cat $input_dir/$strand_file".strand" | awk '{if ($5=="-") print $0}' | cut -f 1 > $flip_file

#Create a file that compare Will's position to position in Plink file, keep variant with difference in position less than 10bp
pos_file=$output/$strand_file.pos
awk -f checkPositions.awk $stem".bim" $input_dir/$strand_file".strand" > $pos_file
if ! [ -z  "$remove_multi" ]; then
  rem_file=$output/$strand_file.rem
  cat $input_dir/$strand_file".multiple" | cut -f 1 > $rem_file 
fi

# We only want to keep variant in strand file
in_file=$output/$strand_file.infile
cat $input_dir/$strand_file".strand" | cut -f 1 > $in_file

#Because Plink only allows you to update one attribute at a time, we need lots of temp
#Plink files
temp_prefix=TEMP_FILE_XX72262628_
temp1=$temp_prefix"1"
temp2=$temp_prefix"2"
if ! [ -z  "$remove_multi" ]; then
  temp3=$temp_prefix"3"
fi

#1. Apply the flip
$PLINK_EXEC  --allow-no-sex --bfile $stem --flip $flip_file --make-bed --out $temp1
if ! [ -z  "$remove_multi" ]; then
  #2. Exclude the SNPs in the pos file, we don't want SNPs more than 10bp difference between Illumina and strand file
  $PLINK_EXEC  --allow-no-sex --bfile $temp1 --exclude $pos_file --make-bed --out $temp2
  #3. Exclude the SNPs in the .multiple file, we don't want SNPs that aren't in the .multiple file
  $PLINK_EXEC  --allow-no-sex --bfile $temp2 --exclude $rem_file --make-bed --out $temp3
  #4. Extract the SNPs in the strand file, we don't want SNPs that aren't in the strand file
  $PLINK_EXEC  --allow-no-sex --bfile $temp3 --extract $in_file --make-bed --out $outstem
else
  #2. Exclude the SNPs in the pos file, we don't want SNPs more than 10bp difference between Illumina and strand file
  $PLINK_EXEC  --allow-no-sex --bfile $temp1 --exclude $pos_file --make-bed --out $temp2
  #3. Extract the SNPs in the strand file, we don't want SNPs that aren't in the strand file
  $PLINK_EXEC  --allow-no-sex --bfile $temp2 --extract $in_file --make-bed --out $outstem
fi

#Now delete any temporary artefacts produced
rm -f $temp_prefix*