do_step3.psh

#!/bin/bash

name=$1

rm -f ${name}.subsam

function do_str1 {
export LANG=C
cut -f 1 ${name}.final | while read line
do
	grep -i -w "^$line" cand_sam/${name}_?_Nmm.sam | cut -d ':' -f 2 >> ${name}.subsam
done
}

do_str1

function do_str2 {
for i in A C G T
do
	myjoin -F 1 -f 1 -m ${name}.final cand_sam/${name}_${i}_Nmm.sam | cut -f 6- >> ${name}.subsam
done
}

do_str2

awk '{print $1,$2,$3,$4,$4+length($5)-3-1}' OFS="\t" ${name}.subsam > ${name}.region	# remove NGG

# GC
sed 's/AGG$//' cand_fa/${name}_A.fa > ${name}.seq
infoseq -nohead -only -name -pgc ${name}.seq > ${name}.gc	# infoseq in EMBOSS (v6.6.0)

Rscript do_moving.r $name