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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) 							   User Commands							   uniq(1)

NAME
uniq - report or filter out repeated lines in a file SYNOPSIS
/usr/bin/uniq /usr/bin/uniq [-c | -d | -u] [-f fields] [-s char] [input_file [output_file]] /usr/bin/uniq [-c | -d | -u] [-n] [+ m] [input_file [output_file]] ksh93 uniq [-cdiu] [-D[delimit]] [-f fields] [-s chars] [-w chars] [input_file [output_file]] uniq [-cdiu] [-D[delimit]] [-n] [+m] [-w chars] [input_file [output_file]] DESCRIPTION
/usr/bin/uniq The uniq utility reads an input file comparing adjacent lines and writes one copy of each input line on the output. The second and succeed- ing copies of repeated adjacent input lines are not written. Repeated lines in the input are not detected if they are not adjacent. ksh93 The uniq built-in in ksh93 is associated with the /bin or /usr/bin path. It is invoked when uniq is executed without a pathname prefix and the pathname search finds a /bin/uniq or /usr/bin/uniq executable. uniq reads an input, comparing adjacent lines, and writing one copy of each input line on the output. The second and succeeding copies of the repeated adjacent lines are not written. If output_file is not specified, uniq writes to standard output. If input_file is not specified, or if input_file is -, uniq reads from standard input, and the start of the file is defined as the current offset. OPTIONS
/usr/bin/uniq The following options are supported by /usr/bin/uniq: -c Precedes each output line with a count of the number of times the line occurred in the input. -d Suppresses the writing of lines that are not repeated in the input. -f fields Ignores the first fields fields on each input line when doing comparisons, where fields is a positive decimal integer. A field is the maximal string matched by the basic regular expression: [[:blank:]]*[^[:blank:]]* If fields specifies more fields than appear on an input line, a null string is used for comparison. +m Equivalent to -s chars with chars set to m. -n Equivalent to -f fields with fields set to n. -s chars Ignores the first chars characters when doing comparisons, where chars is a positive decimal integer. If specified in conjunc- tion with the -f option, the first chars characters after the first fields fields is ignored. If chars specifies more charac- ters than remain on an input line, a null string is used for comparison. -u Suppresses the writing of lines that are repeated in the input. ksh93 The following options are supported by the uniq built-in command is ksh93: -c Outputs the number of times each line occurred along with the line. --count -d Outputs only duplicate lines. --repeated | duplicates -D Outputs all duplicate lines as a group with an empty line delimiter specified by delimit. --all-repeated[=delimit] Specify delimit as one of the following: none Do not delimit duplicate groups. prepend Prepend an empty line before each group. separate Separate each group with an empty line. The value for delimit can be omitted. The default value is none. -f Skips over fields number of fields before checking for uniqueness. A field is the minimal string matching the --skip-fields=fields BRE [[:blank:]]*[^[:blank:]]*. -i Ignore case in comparisons. --ignore-case +m Equivalent to the -s chars option, with chars set to m. -n Equivalent to the -f fields option, with fields set to n. -s Skips over chars number of characters before checking for uniqueness. --skip-chars=chars If specified with the -f option, the first chars after the first fields are ignored. If the chars specifies more characters than are on the line, an empty string is used for comparison. -u Outputs unique lines. --uniq -w Skips over any specified fields and characters, then compares chars number of characters. --check-chars=chars OPERANDS
The following operands are supported: input_file A path name of the input file. If input_file is not specified, or if the input_file is -, the standard input is used. output_file A path name of the output file. If output_file is not specified, the standard output is used. The results are unspecified if the file named by output_file is the file named by input_file. EXAMPLES
Example 1 Using the uniq Command The following example lists the contents of the uniq.test file and outputs a copy of the repeated lines. example% cat uniq.test This is a test. This is a test. TEST. Computer. TEST. TEST. Software. example% uniq -d uniq.test This is a test. TEST. example% The next example outputs just those lines that are not repeated in the uniq.test file. example% uniq -u uniq.test TEST. Computer. Software. example% The last example outputs a report with each line preceded by a count of the number of times each line occurred in the file: example% uniq -c uniq.test 2 This is a test. 1 TEST. 1 Computer. 2 TEST. 1 Software. example% ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of uniq: LANG, LC_ALL, LC_CTYPE, LC_MES- SAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 Successful completion. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: /usr/bin/uniq +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Committed | +-----------------------------+-----------------------------+ |Standard |See standards(5). | +-----------------------------+-----------------------------+ ksh93 +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ |Interface Stability |See below. | +-----------------------------+-----------------------------+ The ksh93 built-in binding to /bin and /usr/bin is Volatile. The built-in interfaces are Uncommitted. SEE ALSO
comm(1), ksh93(1), , pcat(1), sort(1), uncompress(1), attributes(5), environ(5), standards(5) SunOS 5.11 13 Mar 2008 uniq(1)
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