embed python in bash script

Question

I'm pretty new to python and I'm trying to embed it in a bash script. I have the following bash shell script:

#!/bin/bash
while read line
do
 ORD=`echo $line | cut -c 1-7`
 if [[ -r ../FASTA_SEC/COMBI_RAW/${ORD}_COMBI_RAW.fa ]]
 then
 touch ../Results/Log_Files/Log_${ORD}.txt
 for (( win = 2; win < 20; win += 2 )); do
 printf 'The value of win is %d, now entereing inner loop\n' "$win"
 for (( per = 50; per < 100; per += 2 )); do
 printf 'Value of per is %d\n' "$per"
 WCNO=`grep -o "n\|N" ../FASTA_SEC/COMBI_RAW/${ORD}_COMBI_RAW.fa | wc -l`
 WCNF=`grep -o "n\|N" ../Results/COMBI/${ORD}_COMBI/${ORD}_w${win}_p${per}_COMBI.fa | wc -l`
 WCAO=`grep -o "a\|A\|g\|G\|t\|T\|c\|C" ../FASTA_SEC/COMBI_RAW/${ORD}_COMBI_RAW.fa | wc -l`
 WCAF=`grep -o "a\|A\|g\|G\|t\|T\|c\|C" ../Results/COMBI/${ORD}_COMBI/${ORD}_w${win}_p${per}_COMBI.fa | wc -l`
 PERN=`echo print ($WCNO-$WCNF)/$WCNO. | python`
 echo $ORD $PERN
 done
 done
 else
 echo ${ORD}"_COMBI_RAW.fa does not exist"
 fi
done < ./Data_ORD.txt

I would like to carry out this percentage calculation stored in a variable calling python

PERN=`echo print ($WCNO-$WCNF)/$WCNO. | python` 

Parenthesis are giving trouble so i get the following output when i run the bash script:

command substitution: line 17: syntax error near unexpected token `('
command substitution: line 17: `echo print ($WCNO-$WCNF)/$WCNO. | python'

Is it something wrong with bash? operation order are defined with parenthesis in python as far as I know.

Thank you,

Answer 1

bash is interpreting the ( when you don't want it to. You need to enclose the expression you're sending to python in quotes.

PERN=`echo "print ($WCNO-$WCNF)/$WCNO." | python`

If you're curious what bash thought you were doing...

The construct (...) indicates something to run inside a subshell. First, bash would interpolate the variables $WCNO and $WCNF. Then it would try to run the thing in the parens as a command, in a subshell. Unless that string coincidentally exists as a command, bash will complain because the command it tried to find does not exist.

See also this answer on Unix.SE.

• Neuls: Thank you! Nice explanation