Bash looking in different directory for file that isn't referenced in command
When I run the below bash I get the expected output, which is the sum of all matching targets less than 20 in $file1. The filename in the directory is fixed (in bold).
Code:
for file1 in /home/cmccabe/Desktop/test/panel/reads/16-0000_EPIL70.txt ; do
bname=`basename $file1`
pref=${bname%%_*.txt}
awk '{gsub(/[()]/,_)} \
count[$5]==""{ count[$5]=0 }
$7 < 20{ count[$5]++}
END{
for(k in count)
printf "%s %d\n", k, count[k]
}' $file1 > /home/cmccabe/Desktop/test/panel/20x/base/16-0000_allepil70.bed
done
The desired bash is the exact same except the unique numerical digits, 16-0000 are read into a variable {pref}. This is because there can be multiple files with the same extension, but the digits are always unique.
Code:
for file1 in /home/cmccabe/Desktop/test/panel/reads/${pref}_EPIL70.txt ; do
bname=`basename $file1`
pref=${bname%%_*.txt}
awk '{gsub(/[()]/,_)} \
count[$5]==""{ count[$5]=0 }
$7 < 20{ count[$5]++}
END{
for(k in count)
printf "%s %d\n", k, count[k]
}' $file1 > /home/cmccabe/Desktop/test/panel/20x/base/${pref}_allepil70.bed
done
awk: fatal: cannot open file `/home/cmccabe/Desktop/test/panel/reads/16-0000_epil70lessthan20xregions.txt_EPIL70.txt' for reading
The file that it is looking for is not in that directory, but not sure why it is even looking for it as I do not reference it at all in the command or do I? Thank you .
Code:
ls -l /home/cmccabe/Desktop/test/panel/reads
total 10952
-rw-rw-r-- 1 cmccabe cmccabe 11214550 Feb 7 07:27 16-0000_EPIL70.txt
Last edited by cmccabe; 02-07-2017 at 11:49 AM..
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LEARN ABOUT POSIX
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
02-07-2017
.