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ruby -e 'Dir["*"].each_with_index{|x,y| print "#{y+1} #{File.read(x).split.count("AT")}\n"}'

try this,


#!/bin/sh

for i in {1..4}
do
awk 'NR==FNR{a[$5]=++i;next} { if ( $5 in a) {print $0}}' $i.xyz $i.txt > EF_$i
done

try this,

awk 'NR==FNR{a[$5]=++i;next} { if ( $5 in a) {print $0}}' 3.xyz 3.txt

just execute the same code on your files.so 1st and last step will be performed.
1.

#!/bin/ksh
for i in `ls *.txt`
do
nawk '!($4=="AT" && $9>0.10 )' $i > newfile_$i.txt
done


3.

...

Try this:
awk '$4=="AT" && $9 <= 0.1 && $9 >= 0.0' file