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Full Discussion: Rename portion of file based on another file
Top Forums Shell Programming and Scripting Rename portion of file based on another file Post 302583126 by agama on Monday 19th of December 2011 03:59:31 PM
Old 12-19-2011
I don't usually use bash, so I didn't realise this before... seems that the script will work under bash without the typeset -A; have a try and see what happens. I tested it under bash, but didn't notice the complaint about the bad option to typeset.

As for the CRCn issue, I should have suggested this, but thought they were all *1 (I only looked at the first few filenames in your sample, so this is likely my fault). You can use something like this:

Code:
lane_n=${lanename:3:1}   # add this just before the cat command

and when substituting use:
Code:
ColonTrio${lane_n}_

which should take the number from the CRC and append it to ColonTrio.


EDIT: I tested this with bash version 3.2.39 -- if taking away the typeset all together doesn't work, it may be a version difference and another work around will be needed.

---------- Post updated at 15:59 ---------- Previous update was at 15:43 ----------

Here's a solution that should work -- avoids using an associative array in the shell:

Code:
while read old new
do
    eval $old=\"$new\"    # build a list of variables named using old with value that is new. 
done <barcodekey.txt 


find *gz | while IFS="_" read name lanename date sequence lane readpair number
do
    eval xlation=\"\$$sequence\"  # use the old name as a variable to get it's translation.
    if [[ ! -f ColonTrio1_${xlation}_${readpair}.fastq.gz ]]    # not already renamed
    then
        lane_n=${lanename:3:1}    # save the n after CRC
        echo "cat *_${lanename}_*_${sequence}_*_${readpair}* >ColonTrio${lane_n}_${xlation}_${readpair}.fastq.gz"
    fi
done

Last edited by agama; 12-19-2011 at 04:45 PM.. Reason: additional info
This User Gave Thanks to agama For This Post:
anjulka
 

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LEARN ABOUT XFREE86

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)

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