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Full Discussion: Bash to select text and apply it to a selected file in bash
Top Forums Shell Programming and Scripting Bash to select text and apply it to a selected file in bash Post 302982542 by cmccabe on Thursday 29th of September 2016 04:57:30 PM
Old 09-29-2016
Did I add it in the wrong place? Thanks.

Code:
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

 

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LEARN ABOUT DEBIAN

git-symbolic-ref

GIT-SYMBOLIC-REF(1)						    Git Manual						       GIT-SYMBOLIC-REF(1)

NAME

       git-symbolic-ref - Read and modify symbolic refs

SYNOPSIS

       git symbolic-ref [-m <reason>] <name> <ref>
       git symbolic-ref [-q] [--short] <name>

DESCRIPTION

       Given one argument, reads which branch head the given symbolic ref refers to and outputs its path, relative to the .git/ directory.
       Typically you would give HEAD as the <name> argument to see which branch your working tree is on.

       Given two arguments, creates or updates a symbolic ref <name> to point at the given branch <ref>.

       A symbolic ref is a regular file that stores a string that begins with ref: refs/. For example, your .git/HEAD is a regular file whose
       contents is ref: refs/heads/master.

OPTIONS

       -q, --quiet
	   Do not issue an error message if the <name> is not a symbolic ref but a detached HEAD; instead exit with non-zero status silently.

       --short
	   When showing the value of <name> as a symbolic ref, try to shorten the value, e.g. from refs/heads/master to master.

       -m
	   Update the reflog for <name> with <reason>. This is valid only when creating or updating a symbolic ref.

NOTES

       In the past, .git/HEAD was a symbolic link pointing at refs/heads/master. When we wanted to switch to another branch, we did ln -sf
       refs/heads/newbranch .git/HEAD, and when we wanted to find out which branch we are on, we did readlink .git/HEAD. But symbolic links are
       not entirely portable, so they are now deprecated and symbolic refs (as described above) are used by default.

       git symbolic-ref will exit with status 0 if the contents of the symbolic ref were printed correctly, with status 1 if the requested name is
       not a symbolic ref, or 128 if another error occurs.

GIT

       Part of the git(1) suite

Git 1.7.10.4							    11/24/2012						       GIT-SYMBOLIC-REF(1)
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