I am processing text files looking for a string and replacing the first occurrence of the string with something else.
For the text,
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,
I still get the necessary results. When, however, I assign current_name and new_name from a bash array and other bash variables,
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..
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,
so the file is sorted on column 2 and uniq ignores the first column.
For the above data the output would be,
Then I iterate over the array to parse the lines and capture individual names,
When I echo $current_name I get the correct value but it doesn't work with the sed command I posted.
Attention: sed uses RE, so any RE-special character or the / separator will cause a malfunction.
Is the goal to index all the duplicates?
Then consider this robust awk solution
With a trick the dup array discovers the duplicates AND and counts the index (backwards though).
This User Gave Thanks to MadeInGermany For This Post:
One problem might be that your input data do have DOS line terminators (<CR> = 0x0D = ^M = \r); did you try without?
These are unix files, so there shouldn't be an issue with EOL. I am a bit mystified as to why it works from the command line but not from my script.
Quote:
Originally Posted by RudiC
BTW, your approach seems somewhat complicated. Does it do anything else or is its sole purpose to add a counter to the first instance of duplicates?
There are a number of things that need to be done. I need to identify and re-name duplicates in several files. Every name needs to be unique, so I am finding the dups and adding an indexed prefix to each instance. There could be more than one duplicate string.
Quote:
Originally Posted by MadeInGermany
Attention: sed uses RE, so any RE-special character or the / separator will cause a malfunction.
I suspect that something like this may be the issue but I am not sure why RudiC is able to run it.
Quote:
Originally Posted by MadeInGermany
Is the goal to index all the duplicates?
I think your code would work well if I only had one file to change. I need to change the name and then look up the name in several other files and propagate the change so that all files have the revised name.
This is the current script
When I run this on the attached file test_base.txt, I get the printed output I expect,
All of the duplicates are identified and renamed with an indexed prefix. This works very fast and I have each duplicate name in scope in the do loop where I can work on other files.
At this point I am not able to make changes in other files, which is annoying. I am sure that the logic above is overly complex.
Could the problem also be how I am reading the data into the array?
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