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Full Discussion: Add unique identifier from file to filetype in directory
Top Forums Shell Programming and Scripting Add unique identifier from file to filetype in directory Post 302986496 by Don Cragun on Friday 25th of November 2016 11:48:42 PM
Old 11-26-2016
I am fully aware that your current code only processes the contents of one directory. What I asked was whether or not you wanted your script to only process one directory. Since you didn't answer that question, the following script only processes one subdirectory of the directory /home/cmccabe/Desktop/index. (With changes to two lines and removal of a third line in this script, you can make it process files in all of the subdirectories instead of just processing files in one subdirectory.) The subdirectory is specified by an operand passed to your script (which defaults to R_2016_09_21_14_01_15_user_S5-00580-9-Medexome if no operand is given when you invoke this script).

Code:
#!/bin/bash
BaseDir=/home/cmccabe/Desktop/index
TranslationFile=/home/cmccabe/s5_files/identifier/input
SubDir=${1:-R_2016_09_21_14_01_15_user_S5-00580-9-Medexome}

cd "$BaseDir/$SubDir"
printf '%s\n' *.bam *.vcf | awk '
FNR == NR  {
	if(NF == 2)
		old[$2] = $1
	next
}
{	prefix = substr($0, 1, length($0) - 4)
	suffix = substr($0, length($0) - 3)
	if(prefix in old)
		printf("mv \"%s\" \"%s%s\"\n", $0, old[prefix], suffix)
	else	printf("# No translation found for \"%s\"\n", $0)
}' "$TranslationFile" -

which, with the sample data you provided, produces the output:
Code:
mv "MEV21.bam" "IonXpress_007.bam"
mv "MEV22.bam" "IonXpress_008.bam"
mv "MEV23.bam" "IonXpress_009.bam"
mv "MEV21.vcf" "IonXpress_007.vcf"
mv "MEV22.vcf" "IonXpress_008.vcf"
mv "MEV23.vcf" "IonXpress_009.vcf"

If you like the list of command produced by this script, run it again and pipe the output to a shell.

And, as always, if you want to try this on a Solaris/SunOS system, change awk to /usr/xpg4/bin/awk or nawk.
This User Gave Thanks to Don Cragun For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

tk_uid

Tk_GetUid(3tk)						       Tk Library Procedures						    Tk_GetUid(3tk)

__________________________________________________________________________________________________________________________________________________

NAME

       Tk_GetUid, Tk_Uid - convert from string to unique identifier

SYNOPSIS

       #include <tk.h>

       Tk_Uid
       Tk_GetUid(string)

ARGUMENTS

       char *string (in)			 String for which the corresponding unique identifier is desired.
_________________________________________________________________

DESCRIPTION

       Tk_GetUid  returns  the	unique identifier corresponding to string.  Unique identifiers are similar to atoms in Lisp, and are used in Tk to
       speed up comparisons and searches.  A unique identifier (type Tk_Uid) is a string pointer and may be used anywhere that a variable of  type
       "char  *"  could  be  used.   However, there is guaranteed to be exactly one unique identifier for any given string value.  If Tk_GetUid is
       called twice, once with string a and once with string b, and if a and b have the same string value (strcmp(a, b) == 0), then Tk_GetUid will
       return  exactly	the  same Tk_Uid value for each call (Tk_GetUid(a) == Tk_GetUid(b)).  This means that variables of type Tk_Uid may be com-
       pared directly (x == y) without having to call strcmp.  In addition, the return value from Tk_GetUid will have the same string value as its
       argument (strcmp(Tk_GetUid(a), a) == 0).

KEYWORDS

       atom, unique identifier

Tk																    Tk_GetUid(3tk)
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