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Top Forums Shell Programming and Scripting Bash to calculate average of all files in directory and output by part of filename Post 302983014 by Don Cragun on Wednesday 5th of October 2016 03:28:11 PM
Old 10-05-2016
Quote:
Originally Posted by cmccabe
Thank you for the suggestion it lead me to the below which produces the desired result:

Code:
for f in /home/cmccabe/Desktop/20x/percent/*.txt ; do
     bname=$(basename $f)
     pref=${bname%%_base_*.txt}
     awk '{ sum += $2 } END { if (NR > 0) print sum / NR }' $f /home/cmccabe/Desktop/NGS/bed/bedtools/IDP_total_target_length_by_panel/IDP_unix_trim_total_target_length.bed > /home/cmccabe/Desktop/20x/coverage/${pref}_average.txt
done

Thank you for your help Smilie.
Note that instead of starting a subshell for the command substitution and invoking the basename utility for every file you process, you can change:
Code:
     bname=$(basename $f)

to:
Code:
     bname=${f##*/}

to make it more efficient and a little bit faster while getting exactly the same results.
 

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BASENAME(3)						     Linux Programmer's Manual						       BASENAME(3)

NAME
basename, dirname - parse pathname components SYNOPSIS
#include <libgen.h> char *dirname(char *path); char *basename(char *path); DESCRIPTION
Warning: there are two different functions basename() - see below. The functions dirname() and basename() break a null-terminated pathname string into directory and filename components. In the usual case, dirname() returns the string up to, but not including, the final '/', and basename() returns the component following the final '/'. Trail- ing '/' characters are not counted as part of the pathname. If path does not contain a slash, dirname() returns the string "." while basename() returns a copy of path. If path is the string "/", then both dirname() and basename() return the string "/". If path is a NULL pointer or points to an empty string, then both dirname() and basename() return the string ".". Concatenating the string returned by dirname(), a "/", and the string returned by basename() yields a complete pathname. Both dirname() and basename() may modify the contents of path, so it may be desirable to pass a copy when calling one of these functions. These functions may return pointers to statically allocated memory which may be overwritten by subsequent calls. Alternatively, they may return a pointer to some part of path, so that the string referred to by path should not be modified or freed until the pointer returned by the function is no longer required. The following list of examples (taken from SUSv2) shows the strings returned by dirname() and basename() for different paths: path dirname basename /usr/lib /usr lib /usr/ / usr usr . usr / / / . . . .. . .. RETURN VALUE
Both dirname() and basename() return pointers to null-terminated strings. (Do not pass these pointers to free(3).) CONFORMING TO
POSIX.1-2001. NOTES
There are two different versions of basename() - the POSIX version described above, and the GNU version, which one gets after #define _GNU_SOURCE /* See feature_test_macros(7) */ #include <string.h> The GNU version never modifies its argument, and returns the empty string when path has a trailing slash, and in particular also when it is "/". There is no GNU version of dirname(). With glibc, one gets the POSIX version of basename() when <libgen.h> is included, and the GNU version otherwise. BUGS
In the glibc implementation of the POSIX versions of these functions they modify their argument, and segfault when called with a static string like "/usr/". Before glibc 2.2.1, the glibc version of dirname() did not correctly handle pathnames with trailing '/' characters, and generated a segfault if given a NULL argument. EXAMPLE
char *dirc, *basec, *bname, *dname; char *path = "/etc/passwd"; dirc = strdup(path); basec = strdup(path); dname = dirname(dirc); bname = basename(basec); printf("dirname=%s, basename=%s ", dname, bname); SEE ALSO
basename(1), dirname(1) COLOPHON
This page is part of release 3.53 of the Linux man-pages project. A description of the project, and information about reporting bugs, can be found at http://www.kernel.org/doc/man-pages/. GNU
2009-03-30 BASENAME(3)
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