If else script in bash using grep and awk - bash

Question

I am trying to make a script to check if the value snp (column $4 of the test file) is present in another file (map file). If so, print the value snp and the value distance taken from the map file (distance is the column $4 of the map file). If the snp value from the test file is not present in the map file, print the snp value but put a 0 (zero) in the second column as distance value.
The script is:
for chr in {1..22};
do
for snp in awk '{print $4}' test$chr.bim
i=$(grep $snp map$chr.txt | wc -l | awk '{print $1}')
if [[ $i == "0" ]]
then
echo "$snp 0" >> position.$chr
else
distance=$(grep $snp map$chr.txt | awk '{print $4}')
echo "$snp $distance" >> position.$chr
fi
done
done
my map file is made like this:
Chromosome Position(bp) Rate(cM/Mb) Map(cM)
chr22 16051347 8.096992 0.000000
chr22 16052618 8.131520 0.010291
chr22 16053624 8.131967 0.018472
and so on..
my test file is made like this:
22 16051347 0 16051347 C A
22 16052618 0 16052618 G T
22 17306184 0 17306184 T G
and so on..
I'm getting the following syntax errors:
position.sh: line 6: syntax error near unexpected token `i=$(grep $snp map$chr.txt | wc -l | awk '{print $1}')'
position.sh: line 6: `i=$(grep $snp map$chr.txt | wc -l | awk '{print $1}')'
Any tip?

Answer 1

The attempt to use awk as the argument to for is basically a syntax error, and you have a number of syntax problems and inefficiencies here.
Try this:
for chr in {1..22}; do
awk '{print $4}' "test$chr.bim" |
while IFS="" read -r snp; do
if ! grep -q "$snp" "map$chr.txt"; then
echo "$snp 0"
else
awk -v snp="$snp" '
$0 ~ snp { print snp, $4 }' "map$chr.txt"
fi >> "position.$chr"
done
done
The entire thing could probably be further refactored to a single Awk script.
for chr in {1..22}; do
awk 'NR == FNR { ++a[$4]; next }
$2 in a { print a[$2], $4; ++found[$2] }
END { for(k in a) if (!found[k]) print a[k], 0 }' \
"test$chr.bim" "map$chr.txt" >> "position.$chr"
done
The correct for syntax for what I'm guessing you wanted would look like
for snp in $(awk '{print $4}' "test$chr.bim"); do
but this has other problems; see don't read lines with for