Bash to select text and apply it to a selected file in bash

Shell Programming and Scripting
1

In the bash below I am asking the user for a panel and reading that into bed . Then asking the user for a file and reading that into file1 .Is the grep in bold the correct way to apply the selected panel to the file ? I am getting a syntax error. Thank you :slight_smile:

FILESDIR=/home/cmccabe/Desktop/ref/validation/val
PANELDIR=/home/cmccabe/Desktop/ref/validation/panels

PS3="please select a panel: "

cd "$PANELDIR"
select bed in $(ls *.txt)
do    [ "$panel" != "" ] && break
done

PS3="please select a file to analyze with a panel: "

cd "$FILESDIR"
select file1 in $(ls *.vcf)
do    [ "$file1" != "" ] && break
done
      printf "FILE is: ${file1} and will be used filtered to ${panel} \n"
      read -r -p "Is this correct? [y/N] " response
if [[ $response =~ ^[nN][oO]?$ ]]
then
echo 'please try again'  && exit
else

logfile="/home/cmccabe/Desktop/ref/validation/val/process.log"
for f in /home/cmccabe/Desktop/ref/validation/val/$file1 ; do
     echo "Start filter creation: $(date) - File: $f"
     bname=$(basename $f)
     pref=${bname%%_*.vcf}
     grep -wFf /home/cmccabe/Desktop/ref/validation/panels/$panel $f >/home/cmccabe/Desktop/ref/validation/filtered/${pref}_filtered.txt
     echo "End filder creation: $(date) - File: $f"
done >> "$logfile"
line 32: syntax error: unexpected end of file
2

If you would indent your code inside for , while , if , and similar constructs, it would be easier to see that you have an if , then , and else with no fi .

1 Like
3

Did I add it in the wrong place? Thanks.

FILESDIR=/home/cmccabe/Desktop/ref/validation/val
PANELDIR=/home/cmccabe/Desktop/ref/validation/panels

PS3="please select a panel: "

cd "$PANELDIR"
select bed in $(ls *.txt)
do    [ "$bed" != "" ] && break
done

PS3="please select a file to analyze with a panel: "

cd "$FILESDIR"
select file1 in $(ls *.vcf)
do    [ "$file1" != "" ] && break
done
      printf "FILE is: ${file1} and will be used filtered to ${bed} \n"
      read -r -p "Is this correct? [y/N] " response
    if [[ $response =~ ^[nN][oO]?$ ]]
         then
         echo 'please try again'  && exit
    else
    fi
logfile="/home/cmccabe/Desktop/ref/validation/val/process.log"
for f in /home/cmccabe/Desktop/ref/validation/val/$file1 ; do
     echo "Start filter creation: $(date) - File: $f"
     bname=$(basename $f)
     pref=${bname%%_*.txt}
     grep -wFf /home/cmccabe/Desktop/ref/validation/panels/$bed $f >/home/cmccabe/Desktop/ref/validation/filtered/${pref}_filtered.txt
     echo "End filder creation: $(date) - File: $f"
done >> "$logfile"
syntax error near unexpected token `fi
4

I have no idea what you are trying to do with this script. So, I don't know if the fi should follow the following assignment statement or follow the following for loop, or whether you just need to remove the empty else before the fi and leave the fi where it is???

5

then or else in an if construct cannot have empty 'body'.
If you still want to have either a then or an else as stubs with nothing in them, follow this paradigm:

else
:
fi