mp_primer

mp_primer

#!/bin/bash

clear
printf "\n *** MULTIPLEX PCR PRIMER GENERATOR ***"
printf "\n\n !!! 'Primer3 & fastx-toolkit' must be installed on the system.\n\n !!! Both FASTA & .param files must be in this directory \n\n !!! Edit parameters (e.g. size, Tm, and etc) before start\n\n "

printf "\n\n Usage : \n    ./mp_primer.sh FASTA PARAMETER \n\n\n Enter to continue... "

read

printf "\n\n\n  ()()() Running... \n\n"


if [ $2 ]; then
		mkdir tmp
		cd tmp
		cp ../$2 .

		sed 's/ /_/g' ../$1 > $1			# replace spaces to "_" in fasta header
		fasta_formatter -i $1 -o $1.tab -t                        # convert to tab
		cut -f 1 $1.tab | while read line; do grep $line $1.tab > $line.split; done        # split each seq into single files

####################################
# sequence file generator (Add titles to tab. "SEQUENCE_ID=", "SEQUENCE_TEMPLATE=")
		for s in ./*.split
		do
			awk '{print "SEQUENCE_ID="$1,"\n","SEQUENCE_TEMPLATE="$2}' $s | sed 's/ //g' > $s.seq
		done

####################################
# parameter file generator
		for s in ./*.split           # to generate a lis of target sequence (CpG) positions
		do
			cut -f 2 $s | grep -bo cg | sed 's/:/\t/g' | cut -f 1 | awk '{print $1+1",2"}' | tr '\n' ' ' | awk '{print "SEQUENCE_TARGET="$0}' | cat - $2 > $s.param
		done

####################################
# combine sequence & parameter files
		grep ">" $1 | sed 's/>//g'| while read line; do cat $line.split.seq $line.split.param > $line.p3in;done 

####################################
# PRIMER3
		for i in ./*.p3in          # run PRIMER3
		do
			primer3_core $i > $i.p3out
		done

####################################
# PRIMER3 result file
		for r in ./*.p3out
		do
			grep 'ID\|0_SEQUENCE=\|0=\|0_TM=' $r | sed 's/=/\t/g' | cut -f 2 | tr '\n' '\t' | sed 's/,/\t/g' | awk 'BEGIN{FS=OFS="\t"}{print $1,$2,$3,$6-$4+1,$4,$6,$5,$7,$8,$9}'
		done > $1.p3outs

		echo 'ID	Forward	Reverse	Product_Size	Product_Start	Product_End	Len_forward	Len_reverse	Tm_forward	Tm_reverse' | \
		cat - $1.p3outs > ../$1.p3results.tsv

		cd ..
		rm -r tmp/
		clear
		printf "\n\n\n\n   >>> '$INPUT.p3results.tsv' has been generated!\n\n\n\n"


else
	clear
	printf "\n\n   !!! ERROR:: FASTA or parameter file is missing!\n\n"
fi