Bash to select text and apply it to a selected file in bash
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
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 $(ls *.txt)
do [ "$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
Last edited by cmccabe; 09-29-2016 at 05:48 PM..
Reason: fixed typo
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LEARN ABOUT OPENSOLARIS
libbash
LIBBASH(7) libbash Manual LIBBASH(7)NAME
libbash -- A bash shared libraries package.
DESCRIPTION
libbash is a package that enables bash dynamic-like shared libraries. Actually its a tool for managing bash scripts whose functions you may
want to load and use in scripts of your own.
It contains a 'dynamic loader' for the shared libraries ( ldbash(1)), a configuration tool (ldbashconfig(8)), and some libraries.
Using ldbash(1) you are able to load loadable bash libraries, such as getopts(1) and hashstash(1). A bash shared library that can be loaded
using
ldbash(1) must answer 4 requirments:
1. It must be installed in $LIBBASH_PREFIX/lib/bash (default is /usr/lib/bash).
2. It must contain a line that begins with '#EXPORT='. That line will contain (after the '=') a list of functions that the library
exports. I.e. all the function that will be usable after loading that library will be listed in that line.
3. It must contain a line that begins with '#REQUIRE='. That line will contain (after the '=') a list of bash libraries that are
required for our library. I.e. every bash library that is in use in our bash library must be listed there.
4. The library must be listed (For more information, see ldbashconfig(8)).
Basic guidelines for writing library of your own:
1. Be aware, that your library will be actually sourced. So, basically, it should contain (i.e define) only functions.
2. Try to declare all variables intended for internal use as local.
3. Global variables and functions that are intended for internal use (i.e are not defined in '#EXPORT=') should begin with:
__<library_name>_
For example, internal function myfoosort of hashstash library should be named as
__hashstash_myfoosort
This helps to avoid conflicts in global name space when using libraries that come from different vendors.
4. See html manual for full version of this guide.
AUTHORS
Hai Zaar <haizaar@haizaar.com>
Gil Ran <ril@ran4.net>
SEE ALSO ldbash(1), ldbashconfig(8), getopts(1), hashstash(1)colors(1)messages(1)urlcoding(1)locks(1)Linux Epoch Linux
09-29-2016
