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