bash script to modify and extract information - bash

Question

I am creating a bash script to modify and summarize information with grep and sed. But it gets stuck.
#!/bin/bash
# This script extracts some basic information
# from text files and prints it to screen.
#
# Usage: ./myscript.sh </path/to/text-file>
#Extract lines starting with ">#HWI"
ONLY=`grep -v ^\>#HWI`
#replaces A and G with R in lines
ONLYR=`sed -e s/A/R/g -e s/G/R/g $ONLY`
grep R $ONLYR | wc -l

Answer 1

The correct way to write a shell script to do what you seem to be trying to do is:
awk '
!/^>#HWI/ {
gsub(/[AG]/,"R")
if (/R/) {
++cnt
}
END { print cnt+0 }
' "$#"
Just put that in the file myscript.sh and execute it as you do today.
To be clear - the bulk of the above code is an awk script, the shell script part is the first and last lines where the shell just calls awk and passes it the input file names.
If you WANT to have intermediate variables then you can create/print them with:
awk '
!/^>#HWI/ {
only = $0
onlyR = only
gsub(/[AG]/,"R",onlyR)
print "only:", only
print "onlyR:", onlyR
if (/R/) {
++cnt
}
END { print cnt+0 }
' "$#"
The above will work robustly, portably, and efficiently on all UNIX systems.

Answer 2

First of all, and as #fedorqui commented - you're not providing grep with a source of input, against which it will perform line matching.
Second, there are some problems in your script, which will result in unwanted behavior in the future, when you decide to manipulate some data:
Store matching lines in an array, or a file from which you'll later read values. The variable ONLY is not the right data structure for the task.
By convention, environment variables (PATH, EDITOR, SHELL, ...) and internal shell variables (BASH_VERSION, RANDOM, ...) are fully capitalized. All other variable names should be lowercase. Since
variable names are case-sensitive, this convention avoids accidentally overriding environmental and internal variables.
Here's a better version of your script, considering these points, but with an open question regarding what you were trying to do in the last line : grep R $ONLYR | wc -l :
#!/bin/bash
# This script extracts some basic information
# from text files and prints it to screen.
#
# Usage: ./myscript.sh </path/to/text-file>
input_file=$1
# Read lines not matching the provided regex, from $input_file
mapfile -t only < <(grep -v '^\>#HWI' "$input_file")
#replaces A and G with R in lines
for((i=0;i<${#only[#]};i++)); do
only[i]="${only[i]//[AG]/R}"
done
# DEBUG
printf '%s\n' "Here are the lines, after relpace:"
printf '%s\n' "${only[#]}"
# I'm not sure what you were trying to do here. Am I gueesing right that you wanted
# to count the number of R's in ALL lines ?
# grep R $ONLYR | wc -l