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Top Forums Shell Programming and Scripting Rename file using partial match to another Post 303040567 by Chubler_XL on Thursday 31st of October 2019 08:12:52 PM
Old 10-31-2019
I'm really confused why this is not working for you. Let's get rid of the here-string and pipe awk into the read:

Code:
run_dir=$1
for run in "$run_dir" ; do  ## # grab run to operate on desired directory
  uniq=${run_dir##*/}  ## store run with no path as uniq

  awk -F '\n' -v RS="" -v ref="$uniq" '
      $0 ~ ref {
          d=split($0, val);
          for(i=1;i<d;i++) print val[i];
      }' "$run_dir"/../f1 |
  while read from to
  do
     [ -z "$to" ] ||
     (
       cd "$run_dir"/bam
       echo "Rename from:$from to:$to"
       for file in *.bam*
       do
          newname=${file/$from*.bam/${to}_RNA.bam}
          [ -f "$file" ] && [ "$newname" != "$file" ] && mv "$file" "$newname"
       done
     )
  done
done

This User Gave Thanks to Chubler_XL For This Post:
 

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UNIQ(1) 						    BSD General Commands Manual 						   UNIQ(1)

NAME
uniq -- report or filter out repeated lines in a file SYNOPSIS
uniq [-c | -d | -u] [-i] [-f num] [-s chars] [input_file [output_file]] DESCRIPTION
The uniq utility reads the specified input_file comparing adjacent lines, and writes a copy of each unique input line to the output_file. If input_file is a single dash ('-') or absent, the standard input is read. If output_file is absent, standard output is used for output. The second and succeeding copies of identical adjacent input lines are not written. Repeated lines in the input will not be detected if they are not adjacent, so it may be necessary to sort the files first. The following options are available: -c Precede each output line with the count of the number of times the line occurred in the input, followed by a single space. -d Only output lines that are repeated in the input. -f num Ignore the first num fields in each input line when doing comparisons. A field is a string of non-blank characters separated from adjacent fields by blanks. Field numbers are one based, i.e., the first field is field one. -s chars Ignore the first chars characters in each input line when doing comparisons. If specified in conjunction with the -f option, the first chars characters after the first num fields will be ignored. Character numbers are one based, i.e., the first character is character one. -u Only output lines that are not repeated in the input. -i Case insensitive comparison of lines. ENVIRONMENT
The LANG, LC_ALL, LC_COLLATE and LC_CTYPE environment variables affect the execution of uniq as described in environ(7). EXIT STATUS
The uniq utility exits 0 on success, and >0 if an error occurs. COMPATIBILITY
The historic +number and -number options have been deprecated but are still supported in this implementation. SEE ALSO
sort(1) STANDARDS
The uniq utility conforms to IEEE Std 1003.1-2001 (``POSIX.1'') as amended by Cor. 1-2002. HISTORY
A uniq command appeared in Version 3 AT&T UNIX. BSD
December 17, 2009 BSD
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