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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 303013764 by LMHmedchem on Wednesday 28th of February 2018 12:51:42 AM
Old 02-28-2018
Problem getting sed to work with variables
Hello,

I am processing text files looking for a string and replacing the first occurrence of the string with something else.

For the text,
Code:
id	Name
1	methyl-(2-methylpropoxy)-oxoammonium
2	N-amino-N-(methylamino)-2-nitrosoethanamine
3	3-methoxy-3-methyloxazolidin-3-ium
4	1,3-dihydroxypropan-2-yl-methyl-methyleneammonium
5	(1R)-1,2,3,3-tetraamino-2-propen-1-ol
6	2-(ethoxyamino)guanidine
7	O-[(2S)-2-aminoazopropyl]hydroxylamine
8	N-$l^{1}-oxidanyl-N-[(2-methylpropan-2-yl)oxy]methanamine
9	(1R)-1,2,3,3-tetraamino-2-propen-1-ol
10	1-amino-1-ethoxyguanidine

I am replacing the first instance of (1R)-1,2,3,3-tetraamino-2-propen-1-ol with 0_(1R)-1,2,3,3-tetraamino-2-propen-1-ol

If I do the following in sed,

sed '0,/(1R)-1,2,3,3-tetraamino-2-propen-1-ol/s//0_(1R)-1,2,3,3-tetraamino-2-propen-1-ol/' input > output.txt

I get the necessary results.

If I add variables to the command line,
Code:
current_name="(1R)-1,2,3,3-tetraamino-2-propen-1-ol";
new_name="0_(1R)-1,2,3,3-tetraamino-2-propen-1-ol";
sed -e "0,/$current_name/s//$new_name/" input > output.txt

I still get the necessary results. When, however, I assign current_name and new_name from a bash array and other bash variables,

current_name="${FIELD[1]}"
new_name='dup_'$name_count'_'$current_name

I do not get the modified output and the file is unchanged. Apparently sed is not able to match the pattern in the file. There are any number of non-standard characters in the data so I don't know if that is an issue or not. The difference that I can see is that when I assign new_name="0_(1R)-1,2,3,3-tetraamino-2-propen-1-ol", I am able to quote the string but when I assign current_name="${FIELD[1]}" I am not able to quote/escape special characters like ( in the string.

It seems like I just am missing some combination of single and double quotes to do the job but I haven't been able to progress past this.

Suggestions would be appreciated.

LMHmedchem
Last edited by LMHmedchem; 02-28-2018 at 01:56 AM..
 

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LEARN ABOUT OSF1

dxmcreatescrolledcstext

DXmCreateScrolledCSText(3X)											       DXmCreateScrolledCSText(3X)

NAME

       DXmCreateScrolledCSText - Creates a compound string text widget with scroll bars.

SYNOPSIS

       Widget DXmCreateScrolledCSText(
	       Widget parent,
	       char *name,
	       Args *args,
	       Cardinal num_args );

PARAMETERS

       The  identifier	(widget ID) of the parent widget.  The name of the created widget.  The application override argument list.  The number of
       arguments in the application override argument list.

DESCRIPTION

       The DXmCreateScrolledCSText routine creates a compound string text widget with scroll bars.   The  routine  uses  the  same  arguments  and
       resources  as the DXmCreateCSText routine to create a compound string text widget but uses the following resources to create horizontal and
       vertical scroll bars for the widget as well:

       -------------------------------------------------------------------
       Resource 	     Description
       -------------------------------------------------------------------
       XmNscrollHorizontal   Controls whether a scroll	bar  that  allows
			     the user to scroll through text horizontally
			     is added to the compound string text window.
       XmNscrollTopSide      Controls whether the horizontal  scroll  bar
			     is  positioned  at  the  top of the compound
			     string text window.
       XmNscrollVertical     Controls whether a scroll	bar  that  allows
			     the  user	to scroll through text vertically
			     is added to the compound string text window.
       XmNscrollLeftSide     Controls whether the vertical scroll bar  is
			     placed  on  the  left  side  of the compound
			     string text window.
       -------------------------------------------------------------------

   Inherited Resources
       The DXmCreateScrolledCSText routine inherits behaviour and resources from the following superclasses:

       Core Resource Set XmPrimitive Resource Set DXmScrolledCSText Resource Set

RETURN VALUES

       The identifier (widget ID) of the created compound string text widget.

SEE ALSO

       DXmCreateCSText(3X)

														       DXmCreateScrolledCSText(3X)
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