Selective replace

Thread Tools Search this Thread
# 8  
i am getting error...

This is brief desciption of what i did
original file
sat_1_g3_g_0_8540         .       FFF     1       15501   .       .       .       ID=sat_1_g3_g_0_8540;parentName=sat_1_g3_g_0_8540;Al=sat_1_g2_g_0_8540;
sat_1_g3_g_2_8510         .       FFF     1       25501   .       .       .       ID=sat_1_g3_g_2_8510;parentName=sat_1_g3_g_2_8510;Al=sat_1_g1_g_2_8510;

I used
sed 's/^sat_1_g3_g_[02]/string/' infile >sortedfile

I think it took off the tab thing and replaced it by spaces.
I did a mistake somewhere dont know where. Tabs are important as far as my follwing codes are concered since they wont work on spaces.
Then replaced FFF by seq using
awk '$3=="FFF"{$3="seq"}1' infile

I dont know which of these replaced my tabs with spaces.Could some 1 help ?

Thanks a lot

---------- Post updated at 10:33 PM ---------- Previous update was at 10:30 PM ----------

Final result that i want
string_8540       .       seq     1       15501   .       .       .       ID=sat_1_g3_g_0_8540;parentName=sat_1_g3_g_0_8540;Al=sat_1_g2_g_0_8540;
string_8510       .       seq     1       25501   .       .       .       ID=sat_1_g3_g_2_8510;parentName=sat_1_g3_g_2_8510;Al=sat_1_g1_g_2_8510;

I want to retain all tabs .I dont know where did i go wrong.Smilie

Last edited by Scrutinizer; 01-22-2013 at 01:59 AM.. Reason: code tags
# 9  
The sed command I gave you will not modify the field separators.

The awk script bipinajith provided changed the tabs used as field separators in your input to spaces in its output. Change his script to:
awk 'BEGIN{FS=OFS="\t"}$3=="FFF"{$3="seq"}1' infile

and your tabs will be preserved.

Last edited by Don Cragun; 01-24-2013 at 09:10 PM.. Reason: remove extraneous ]
# 10  
Is there a way I could attach my file on this .
Coz i couldnt resolve the issue

# 11  
Is there any other method for doing the same?
# 12  
Originally Posted by siya@
Is there any other method for doing the same?
As I was checking out what I suggested in message #9 in this thread, I found that had accidentally included a trailing "]". I have edited that message to remove the extraneous character and it is working for me. Please try it. If it doesn't work, show us the input you gave it, the output you got from it, and the output you need from it.

Previous Thread | Next Thread
Thread Tools Search this Thread
Search this Thread:
Advanced Search

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Selective replace and delete

Hi My input file looks like this: >BAHMI01000090.1 Details of the shopping list 9800 item00090, whole set of listed artifacts and objects >BAHMI01050012.1 Details of the shopping list 9800 item02310, whole set of listed artifacts and objects >BAHMI01070078.1 Details of the shopping list ... (5 Replies)
Discussion started by: sonia102
5 Replies

2. UNIX for Dummies Questions & Answers

SQL selective replace

Hi I have a table which looks like this id | name | length | clone | null 1 | string 1 | 12345643 | string 1 | NULL | 2 | string 2 | 2345612 | string 2 | NULL | 3 | string 3 | 3421556 | string 3 | NULL | 4 | string 4 | 1236742 | string 4 | NULL | 5 | string 5 | 2312677 | string 5 | NULL |... (2 Replies)
Discussion started by: rsi.245
2 Replies

3. Shell Programming and Scripting

Selective Replace awk column values

Hi, I have the following data: 2860377|"DATA1"|"DATA2"|"65343"|"DATA2"|"DATA4"|"11"|"DATA5"|"DATA6"|"65343"|"DATA7"|"0"|"8"|"1"|"NEGATIVE" 32340377|"DATA1"|"DATA2"|"65343"|"DATA2"|"DATA4"|"11"|"DATA5"|"DATA6"|"65343"|"DATA7"|"0"|"8"|"1"|"NEG-DID"... (3 Replies)
Discussion started by: sdohn
3 Replies

4. UNIX for Dummies Questions & Answers

Selective Replacements: Using sed or awk to replace letters with numbers in a very specific way

Hello all. I am a beginner UNIX user who is using UNIX to work on a bioinformatics project for my university. I have a bit of a complicated issue in trying to use sed (or awk) to "find and replace" bases (letters) in a genetics data spreadsheet (converted to a text file, can be either... (3 Replies)
Discussion started by: Mince
3 Replies

5. Shell Programming and Scripting

Selective grep

I have to grep out only email address from a column. It has characters appended and prepended F=<> <> ( <> Whatever added before and after email, I should be able to grep out only emails. (9 Replies)
Discussion started by: anil510
9 Replies

6. UNIX for Dummies Questions & Answers

Help with selective ls

Hi all :wall: Can anyone advise how do I use ls to do a selective amd sorted listing of file that I want to have as below? Am looking for files that are named as log_<nnnn>.txt, where <nnnn> are numeric, i.e. I want to have a listing sorted from the newest to the oldest of files that... (7 Replies)
Discussion started by: newbie_01
7 Replies

7. UNIX for Dummies Questions & Answers

selective grep

Hello, I have been using the command below for file manipulation. while read A B; do grep $f1; done < f2 > f3 So, if a certain string is found in f2 (for ex; DOG243435) and it is also present in f1, then print that string plus the contents of the line in which it was found onto f3. ... (6 Replies)
Discussion started by: verse123
6 Replies

8. Shell Programming and Scripting

selective printing

hi all from below text "abcd,SYS_12345,xyz,PQR, ," I want to print only "abcd,SYS,xyz,PQR, ," i.e. taking only first three 3 chars from 2 string of comma separated file thanks (4 Replies)
Discussion started by: JoeColeEPL9
4 Replies

9. UNIX for Advanced & Expert Users

Selective Umask

Hi, We have umask 022 in /etc/profile for security reasons. But I want have some other umask for selected users. how to achieve this? Regards (3 Replies)
Discussion started by: baanprog
3 Replies

10. Shell Programming and Scripting

echo is selective?

i tried to ask about this earlier, but didn't explain well enough. From a script, i issue the following: echo `pgp --encrypt filename --recipient public-key` The result is perfect. The encrypted file is in the directory just as if i'd issued the pgp command from the command line. However,... (0 Replies)
Discussion started by: rgard
0 Replies

Featured Tech Videos