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Full Discussion: Rename file using partial match to another
Top Forums Shell Programming and Scripting Rename file using partial match to another Post 303040259 by Chubler_XL on Friday 25th of October 2019 04:16:41 PM
Old 10-25-2019
Don't know what that "after the script executes" is showing. Are your filenames ending up with spaces in the etc. like shown above?

Here is the script I'm using:

Code:
dir=/path/to/run/
for run in "$dir"/R_2019* ; do  ## # matching "R_2019*" to operate on desired directory and expand
  uniq=${run##*/}  ## store run with no path as s5
  while read from to
  do
     (
       cd "$dir"/"$uniq"/data
       for file in *.bam*
       do
          newname=${file/$from*.bam/${to}_test.bam}
          [ -f "$file" ] && [ "$newname" != "$file" ] && mv "$file" "$newname"
       done
     )
  done <<<$(
     awk -F '\n' -v RS="" -v ref="$uniq" '
         $0 ~ ref {
             d=split($0, val);
             for(i=1;i<d;i++) print val[i];
          }' "$dir"/f1
  )  ## loop through f1 for unique run and populate from and to
done

And here is my test:
Code:
$ find /path/to/run -type f -print
/path/to/run/f1
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0402_xxx.xxx_xxx.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0402_xxx.xxx_xxx.bam.bai
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0404_xxx.xxx_xxx.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/IonCode_0404_xxx.xxx_xxx.bam.bai
$ ./cmccabe_rename 
$ find /path/to/run -type f -print
/path/to/run/f1
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/22-2222-zz-zzzz-zzz_test.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-126-xxx_xxx_xxx_xxx_xx_xx_xx/data/22-2222-zz-zzzz-zzz_test.bam.bai
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/00-0000-xxx-xxx-xxx_test.bam
/path/to/run/R_2019_00_00_00_00_00_xxxx_xx1-127-xxx_xxx_xxx_xxx_xx_xx_xx/data/00-0000-xxx-xxx-xxx_test.bam.bai

This User Gave Thanks to Chubler_XL For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

ocamlmklib

OCAMLMKLIB(1)						      General Commands Manual						     OCAMLMKLIB(1)

NAME

       ocamlmklib - generate libraries with mixed C / Caml code.

SYNOPSIS

       ocalmklib [options] files

DESCRIPTION

       The  ocamlmklib	command  facilitates the construction of libraries containing both Caml code and C code, and usable both in static linking
       and dynamic linking modes.

OPTIONS

       -h, --help
	      Show summary of options.

       -cclib lib
	      C library passed to ocamlc -a or ocamlopt(1) -a only.

       -ccopt opt
	      C option passed to ocamlc(1) -a or ocamlopt(1) -a only.

       -custom
	      Disable dynamic loading.

       -dllpath dir
	      Add dir to the run-time search path for DLLs.

       -I dir Add dir to the path searched for Caml object files.

       -failsafe
	      Fall back to static linking if DLL construction failed.

       -ldopt opt
	      C option passed to the shared linker only.

       -linkall
	      Build Caml archive with link-all behavior.

       -llib  Specify a dependent C library.

       -Ldir  Add dir to the path searched for C libraries.

       -ocamlc cmd
	      Use cmd in place of ocamlc(1).

       -ocamlopt cmd
	      Use cmd in place of ocamlopt(1).

       -o name
	      Generated Caml library is named name.cma or name.cmxa.

       -oc name
	      Generated C library is named dllname.so or libname.a.

       -rpath dir
	      Same as -dllpath dir.

       -Rdir  Same as -rpath.

       -verbose
	      Print commands before executing them.

       -Wl, -rpath dir
	      Same as -dllpath dir.

       -Wl, -rpath -Wl dir
	      Same as -dllpath dir.

       -Wl, -Rdir
	      Same as -dllpath dir.

       -Fdir  Specify a framework directory (MacOSX).

       -framework name
	      Use framework name (MacOSX).

SEE ALSO

       ocamlc(1), ocamlopt(1).

AUTHOR

       This manual page was written by Samuel Mimram <samuel.mimram@ens-lyon.org>, for the Debian project (but may be used by others).

								  August 19, 2004						     OCAMLMKLIB(1)
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