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grepping something won't be good idea of doing this work..

try this (replace your whole script with this.. :))

awk '!X[$1]++{print $1}' file > scaffolds
while read line
do
awk -v...

Try something like this

sort -nk2 file | awk '{if($2 == s){print P;k=1}else if(1==k){print P;k=0;}}
{s=$3;P=$0}' To decide tolerance difference use
sort -nk2 file | awk -v tol="5"...

Like this?
cd /wherever/files/are
find . -type f -name '*.net'|while IFS='/' read dummy a
do
echo paste "$a" "${a/%net/dat}"
done > output
Remove the echo if this is working as expected.

Hi,

another way;

cat YUORFILE.txt | awk -F" " '{ if ( FNR == 1 ) {a=$0;getline} ; {print a"\t"$0;a=$0} }'

Could I suggest something like:-
prev=""
while read line
do
if [ "$prev" != "" ]
then
echo "$prev\t$line"
fi
prev="$line"
done < imput

The plan here being that for each...