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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 302583092 by agama on Monday 19th of December 2011 02:15:44 PM
Old 12-19-2011
Actually, you can do this with a few changes to your script by building a translation list from your .txt file and using that to change the sequence number. I assume that CRC1 was to become ColonTrio1; wasn't quite sure based on your description.

Code:
typeset -A xlate            # must declare an associative array
while read old new          # build a translation list from old to new
do
    xlate[$old]=$new       # translation table
done <barcodekey.txt     # read in from your old to new translation file

find *gz | while IFS="_" read name lanename date sequence lane readpair number
do
    if [[ ! -f ColonTrio1_${xlate[$sequence]}}_${readpair}.fastq.gz ]] #merge and rename 
    then
        echo "cat *_${lanename}_*_${sequence}_*_${readpair}* >ColonTrio1_${xlate[$sequence]}}_${readpair}.fastq.gz"
    fi
done

I put the 'real' commands in an echo for testing -- it will print out what it would do without really doing it so you can validate before doing damage with the mv command etc. There will probably be many more commands echoed as multiple files found that generate the same merged file will test true in the if, where when running things for real the first file that results in a merge will supress additional files which were merged in. (Hope that makes sense)
Last edited by agama; 12-19-2011 at 03:22 PM.. Reason: typo -- clarification
 

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LEARN ABOUT CENTOS

xtuninstalltranslations

XtParseTranslationTable(3)					   XT FUNCTIONS 					XtParseTranslationTable(3)

NAME

       XtParseTranslationTable, XtAugmentTranslations, XtOverrideTranslations, XtUninstallTranslations - manage translation tables

SYNTAX

       XtTranslations XtParseTranslationTable(String table);

       void XtAugmentTranslations(Widget w, XtTranslations translations);

       void XtOverrideTranslations(Widget w, XtTranslations translations);

       void XtUninstallTranslations(Widget w);

ARGUMENTS

       table	 Specifies the translation table to compile.

       translations
		 Specifies the compiled translation table to merge in (must not be NULL).

       w	 Specifies the widget into which the new translations are to be merged or removed.

DESCRIPTION

       The XtParseTranslationTable function compiles the translation table into the opaque internal representation of type XtTranslations.  Note
       that if an empty translation table is required for any purpose, one can be obtained by calling XtParseTranslationTable and passing an empty
       string.

       The XtAugmentTranslations function nondestructively merges the new translations into the existing widget translations.  If the new transla-
       tions contain an event or event sequence that already exists in the widget's translations, the new translation is ignored.

       The XtOverrideTranslations function destructively merges the new translations into the existing widget translations.  If the new transla-
       tions contain an event or event sequence that already exists in the widget's translations, the new translation is merged in and override
       the widget's translation.

       To replace a widget's translations completely, use XtSetValues on the XtNtranslations resource and specify a compiled translation table as
       the value.

       The XtUninstallTranslations function causes the entire translation table for widget to be removed.

SEE ALSO

       XtAppAddActions(3), XtCreatePopupShell(3), XtParseAcceleratorTable(3), XtPopup(3)
       X Toolkit Intrinsics - C Language Interface
       Xlib - C Language X Interface

X Version 11							    libXt 1.1.4 					XtParseTranslationTable(3)
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