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
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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.
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LEARN ABOUT REDHAT
dos2unix
dos2unix(1) General Commands Manual dos2unix(1)NAME
dos2unix - DOS/MAC to UNIX text file format converter
SYNOPSYS
dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]
Options:
[-hkqV] [--help] [--keepdate] [--quiet] [--version]
DESCRIPTION
This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.
OPTIONS
The following options are available:
-h --help
Print online help.
-k --keepdate
Keep the date stamp of output file same as input file.
-q --quiet
Quiet mode. Suppress all warning and messages.
-V --version
Prints version information.
-c --convmode convmode
Sets conversion mode. Simulates dos2unix under SunOS.
-o --oldfile file ...
Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.
-n --newfile infile outfile ...
New file mode. Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
used or you WILL lost your files.
EXAMPLES
Get input from stdin and write output to stdout.
dos2unix
Convert and replace a.txt. Convert and replace b.txt.
dos2unix a.txt b.txt
dos2unix -o a.txt b.txt
Convert and replace a.txt in ASCII conversion mode. Convert and replace b.txt in ISO conversion mode. Convert c.txt from Mac to Unix
ascii format.
dos2unix a.txt -c iso b.txt
dos2unix -c ascii a.txt -c iso b.txt
dos2unix -c mac a.txt b.txt
Convert and replace a.txt while keeping original date stamp.
dos2unix -k a.txt
dos2unix -k -o a.txt
Convert a.txt and write to e.txt.
dos2unix -n a.txt e.txt
Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.
dos2unix -k -n a.txt e.txt
Convert and replace a.txt. Convert b.txt and write to e.txt.
dos2unix a.txt -n b.txt e.txt
dos2unix -o a.txt -n b.txt e.txt
Convert c.txt and write to e.txt. Convert and replace a.txt. Convert and replace b.txt. Convert d.txt and write to f.txt.
dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt
DIAGNOSTICS BUGS
The program does not work properly under MSDOS in stdio processing mode. If you know why is that so, please tell me.
AUTHORS
Benjamin Lin - <blin@socs.uts.edu.au>
Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>
MISCELLANY
Tested environment:
Linux 1.2.0 with GNU C 2.5.8
SunOS 4.1.3 with GNU C 2.6.3
MS-DOS 6.20 with Borland C++ 4.02
Suggestions and bug reports are welcome.
SEE ALSO unix2dos(1)mac2unix(1)1995.03.31 dos2unix v3.0 dos2unix(1)
06-18-2016
.