No, I am just trying to selct one file in the directory and save it in a new directory. You are correct a loop is not needed.
Search directory with files
Code:
file1.txt
file2.txt
file3.txt
file1.txt is selected and saved in the new directory (/home/cmccabe/Desktop/NGS/panels/reads/)
So do I just need to read that selection into a variable and pass that to the new directory, or is there a better way? Thank you .
Maybe:
Code:
# select file
printf "please select a file to analyze with entered gene or genes \n"
select file in $(cd /home/cmccabe/Desktop/NGS/API/test/bedtools;ls);do break;done
echo $file "will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for vizulization, and calculate 20x and 30x coverage for the entered gene(s)"
logfile=/home/cmccabe/Desktop/NGS/API/test/process.log
for file in /home/cmccabe/Desktop/NGS/API/test/bedtools/$file; do
echo "Start selcted file creation: Date: $(date) - File: $file"
bname=$(basename $file)
pref=${bname%%.txt}
mv "$file" /home/cmccabe/Desktop/NGS/panels/reads/${pref}_OTHER.txt
echo "End selected file creation: $(date) - File: $file"
done >> "$logfile"
error
Code:
file1.txt will be used to filter reads, identify target bases and genes less than 20 and 30 reads, create a low coverage bed for visualization, and calculate 20x and 30x coverage for the entered gene(s)
mv: cannot move ‘/home/cmccabe/Desktop/NGS/API/test/bedtools/file1.txt’ to ‘/home/cmccabe/Desktop/NGS/panels/reads/file1_OTHER.txt’: No such file or directory
Last edited by cmccabe; 06-18-2016 at 10:39 AM..
Reason: edited bash
Hi,
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Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
Hi there.
i have created a program that in the end it will give output like this
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#!/bin/bash
X=(2H 4S 10D QC JD 9H 8S)
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Discussion started by: cogiz
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LEARN ABOUT HPUX
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
06-18-2016
.