bash - Why is this command within my code giving different result than the same command in terminal? -

**edit: okay, i've tried implementing everyone's advice far.

-i've added quotes around each variable "$1" , "$codon" avoid whitespace.

-i've added -ioc flag grep avoid caps.

-i tried using tr -d' ', leads runtime error because says -d' ' invalid option.

unfortunately still seeing same problem. or different problem, tells me every codon appears once. different kind of wrong.

thanks far - i'm still open new ideas. i've updated code below.**

i have bash script supposed count permutations of (a c g t) in given file.

one line of script not giving me desired result , don't know why - because can enter exact same line of code in command prompt , desired result.

the line, executed in command prompt, is:

cat dnafile | grep -o gct | wc -l 

this line tells me how many times regular expression "gct" appears in file dnafile. when run command result 10 (which accurate).

in code itself, run modified version of same command:

cat $1 | grep -o $codon | wc -l 

where $1 file name, , $codon 3-letter combination. when run within program, answer 0 (which decidedly not accurate).

i hoping 1 of fine gents enlighten lost soul why not working expected.

thank very, much!

my code:

#!/bin/bash #countcodons <dnafile> counts occurances of each codon in sequence contained within <dnafile>    if [[ $# != 1 ]]      echo "format is: countcodons <dnafile>"     exit fi  nucleos=(a c g t) allcods=()  #mix , match nucleotides create codons  x in {0..3}      y in {0..3}              z in {0..3}                      perm=${nucleos[$x]}${nucleos[$y]}${nucleos[$z]}                  allcods=("${allcods[@]}" "$perm")          done     done done   #for each codon, use grep count # of occurances in file  len=${#allcods[*]}  (( n=0; n<len; n++ ))     codon=${allcods[$n]}     occs=`cat "$1" | grep -ioc "$codon" | wc -l`      echo "$codon appears: $occs"     #   if (( $occs > 0 )) #   #       echo "$codon : $occs" #   fi done  exit 

you're generating sequences in lowercase. code greps gct, not gct. want add -i switch grep. try:

occs=`grep -ioc $codon $1`