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Full Discussion: Problem getting sed to work with variables
Top Forums Shell Programming and Scripting Problem getting sed to work with variables Post 303013790 by LMHmedchem on Wednesday 28th of February 2018 11:31:24 AM
Old 02-28-2018
Quote:
Originally Posted by RudiC
What's the contents of ${FIELD[1]}? How did you define it?
The script begins by reading a file and looking for duplicate values in a specific column. These are retrieved by,
Code:
# set input field separator to newline so each line is stored in an array element
IFS=$'\n'
# use sort and uniq to output duplicate lines in to array
dup_list=( $(cat "$base_file" | sort -k2 | uniq  -f1 -D) )

so the file is sorted on column 2 and uniq ignores the first column.

For the above data the output would be,
Code:
5	(1R)-1,2,3,3-tetraamino-2-propen-1-ol
9	(1R)-1,2,3,3-tetraamino-2-propen-1-ol

Then I iterate over the array to parse the lines and capture individual names,
Code:
for dup_name in "${dup_list[@]}"
do
   # parse on tab
   unset FIELD; IFS=$'\t' read -a FIELD <<< "$dup_name"
   # assign second column to current name
   current_name="${FIELD[1]}"
done

When I echo $current_name I get the correct value but it doesn't work with the sed command I posted.

LMHmedchem
 

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LEARN ABOUT LINUX

join

JOIN(1) 							   User Commands							   JOIN(1)

NAME

       join - join lines of two files on a common field

SYNOPSIS

       join [OPTION]... FILE1 FILE2

DESCRIPTION

       For  each  pair of input lines with identical join fields, write a line to standard output.  The default join field is the first, delimited
       by whitespace.  When FILE1 or FILE2 (not both) is -, read standard input.

       -a FILENUM
	      print unpairable lines coming from file FILENUM, where FILENUM is 1 or 2, corresponding to FILE1 or FILE2

       -e EMPTY
	      replace missing input fields with EMPTY

       -i, --ignore-case
	      ignore differences in case when comparing fields

       -j FIELD
	      equivalent to `-1 FIELD -2 FIELD'

       -o FORMAT
	      obey FORMAT while constructing output line

       -t CHAR
	      use CHAR as input and output field separator

       -v FILENUM
	      like -a FILENUM, but suppress joined output lines

       -1 FIELD
	      join on this FIELD of file 1

       -2 FIELD
	      join on this FIELD of file 2

       --check-order
	      check that the input is correctly sorted, even if all input lines are pairable

       --nocheck-order
	      do not check that the input is correctly sorted

       --header
	      treat the first line in each file as field headers, print them without trying to pair them

       --help display this help and exit

       --version
	      output version information and exit

       Unless -t CHAR is given, leading blanks separate fields and are ignored, else fields are separated by CHAR.  Any FIELD is  a  field  number
       counted	from 1.  FORMAT is one or more comma or blank separated specifications, each being `FILENUM.FIELD' or `0'.  Default FORMAT outputs
       the join field, the remaining fields from FILE1, the remaining fields from FILE2, all separated by CHAR.

       Important: FILE1 and FILE2 must be sorted on the join fields.  E.g., use ` sort -k 1b,1 ' if `join' has no options, or use ` join -t  ''  '
       if  `sort'  has no options.  Note, comparisons honor the rules specified by `LC_COLLATE'.  If the input is not sorted and some lines cannot
       be joined, a warning message will be given.

AUTHOR

       Written by Mike Haertel.

REPORTING BUGS

       Report join bugs to bug-coreutils@gnu.org
       GNU coreutils home page: <http://www.gnu.org/software/coreutils/>
       General help using GNU software: <http://www.gnu.org/gethelp/>
       Report join translation bugs to <http://translationproject.org/team/>

COPYRIGHT

       Copyright (C) 2010 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       comm(1), uniq(1)

       The full documentation for join is maintained as a Texinfo manual.  If the info and join programs are properly installed at your site,  the
       command

	      info coreutils 'join invocation'

       should give you access to the complete manual.

GNU coreutils 8.5						   February 2011							   JOIN(1)
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