Sponsored Content
Top Forums Shell Programming and Scripting awk to add symbol to specific field Post 302985959 by cmccabe on Thursday 17th of November 2016 10:52:17 AM
Old 11-17-2016
awk to add symbol to specific field

Trying to use awk to add a . to $4. The input and output is tab-delimeted, but the awk seems to add a . in front of $5 and is space-delimeted. It seems close, but I am not able to produce the desired output. Thank you Smilie.

file
Code:
chr1    948895    949015    chr1:948895-949015     ISG15
chr1    949311    949431    chr1:949311-949431     ISG15
chr1    949431    949551    chr1:949431-949551     ISG15

awk with current output
Code:
awk -F'\t' -v OFS='\t' '{$5="."$5;print $0}' file
chr1    948895    949015    chr1:948895-949015    . ISG15
chr1    949311    949431    chr1:949311-949431    . ISG15
chr1    949431    949551    chr1:949431-949551    . ISG15

desired output
Code:
chr1    948895    949015    chr1:948895-949015     .     ISG15
chr1    949311    949431    chr1:949311-949431     .     ISG15
chr1    949431    949551    chr1:949431-949551     .     ISG15

Maybe not the best, but seems to work:
Code:
awk -F'\t' -v OFS='\t' '{print $1, $2, $3 ,".", $4, $5}' file


Last edited by cmccabe; 11-17-2016 at 12:34 PM.. Reason: add possible solution
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk field equal something, then add something to the field

Hi Everyone, a.txt a b c 1 e e e e e a b c 2 e e e e e the output is a b c 1 e e e e e a 00b c 2 e e e e e when 4th field = '2', then add '00' in the front of 2nd field value. Thanks (9 Replies)
Discussion started by: jimmy_y
9 Replies

2. Shell Programming and Scripting

awk how to replace specific field with new value

I need to replace specific field (x) in a table with new value (y): Input: 1 2 3 4 5 x 6 7 8 9 0 0 Output: 1 2 3 4 5 y 6 7 8 9 0 0 I have no idea how to do this. (10 Replies)
Discussion started by: setepo
10 Replies

3. Shell Programming and Scripting

Replace specific field on specific line sed or awk

I'm trying to update a text file via sed/awk, after a lot of searching I still can't find a code snippet that I can get to work. Brief overview: I have user input a line to a variable, I then find a specific value in this line 10th field in this case. After asking for new input and doing some... (14 Replies)
Discussion started by: crownedzero
14 Replies

4. Shell Programming and Scripting

How to print with awk specific field different from specific character?

Hello, i need help with awk. I have this file: cat number DirB port 67 er_enc_out 0 er_bad_os 0 DirB port 71 er_enc_out 56 er_bad_os 0 DirB port 74 er_enc_out 0 er_bad_os 0 DirB port 75 ... (4 Replies)
Discussion started by: elilmal
4 Replies

5. Shell Programming and Scripting

awk to replace a specific field in certain condition

Hi, I have a file like below PRUM,67016800 ,CC ,C1,67016800 , ,Y,Y,2 ,CK,BX,FOX ,00000001,EA,00000001,20141120 00:00:00, ,N,Y,Y,CK ABCDEF... (7 Replies)
Discussion started by: mady135
7 Replies

6. Shell Programming and Scripting

Add value in specific field

Gents, I have many files to change increasing 40000 in specific field. Can you help me with a command with sed or awk to fix this problem. Where the the field has Marker FDU. I need to add 40000 plus example Marker FDU 27152.00 Marker FDU 67152.00 I should... (4 Replies)
Discussion started by: jiam912
4 Replies

7. Shell Programming and Scripting

Add tab after digit in specific field in file

I am trying to add a tab after the last digit in $3 in the input. The grep below is all I can think off. Thank you :) sed -n 's/:/&/p' input input chr1 955542 955763AGRN-6|gc=75 chr1 957570 957852AGRN-7|gc=61.2 chr1 976034 976270AGRN-9|gc=74.5 desired output chr1... (5 Replies)
Discussion started by: cmccabe
5 Replies

8. Shell Programming and Scripting

sed to add field heards to specific fields

I have tab delimited input that prints out in the format below: I am trying to add field headers to $5 and $6. Not sure if sed is the best tool but my attempt is below. Thank you :). $5 = REF $6 = ALT file ID CHR START STOP 123 1 100 200 A ... (6 Replies)
Discussion started by: cmccabe
6 Replies

9. Shell Programming and Scripting

awk to update specific value in file with match and add +1 to specific digit

I am trying to use awk to match the NM_ in file with $1 of id which is tab-delimited. The NM_ will always be in the line of file that starts with > and be after the second _. When there is a match between each NM_ and id, then the value of $2 in id is substituted or used to update the NM_. Each NM_... (3 Replies)
Discussion started by: cmccabe
3 Replies

10. Shell Programming and Scripting

awk to add lines with symbol to output file

In the awk below which does execute I get output that is close, except for all the lines that start with a # are removed. Some lines have one others two or three and after the script adds the ID= to the fields below the pattern in the awk, I can not seem to add the # lines back to the output. ... (5 Replies)
Discussion started by: cmccabe
5 Replies
A2P(1)							 Perl Programmers Reference Guide						    A2P(1)

NAME
a2p - Awk to Perl translator SYNOPSIS
a2p [options] [filename] DESCRIPTION
A2p takes an awk script specified on the command line (or from standard input) and produces a comparable perl script on the standard output. OPTIONS Options include: -D<number> sets debugging flags. -F<character> tells a2p that this awk script is always invoked with this -F switch. -n<fieldlist> specifies the names of the input fields if input does not have to be split into an array. If you were translating an awk script that processes the password file, you might say: a2p -7 -nlogin.password.uid.gid.gcos.shell.home Any delimiter can be used to separate the field names. -<number> causes a2p to assume that input will always have that many fields. -o tells a2p to use old awk behavior. The only current differences are: o Old awk always has a line loop, even if there are no line actions, whereas new awk does not. o In old awk, sprintf is extremely greedy about its arguments. For example, given the statement print sprintf(some_args), extra_args; old awk considers extra_args to be arguments to "sprintf"; new awk considers them arguments to "print". "Considerations" A2p cannot do as good a job translating as a human would, but it usually does pretty well. There are some areas where you may want to examine the perl script produced and tweak it some. Here are some of them, in no particular order. There is an awk idiom of putting int() around a string expression to force numeric interpretation, even though the argument is always integer anyway. This is generally unneeded in perl, but a2p can't tell if the argument is always going to be integer, so it leaves it in. You may wish to remove it. Perl differentiates numeric comparison from string comparison. Awk has one operator for both that decides at run time which comparison to do. A2p does not try to do a complete job of awk emulation at this point. Instead it guesses which one you want. It's almost always right, but it can be spoofed. All such guesses are marked with the comment ""#???"". You should go through and check them. You might want to run at least once with the -w switch to perl, which will warn you if you use == where you should have used eq. Perl does not attempt to emulate the behavior of awk in which nonexistent array elements spring into existence simply by being referenced. If somehow you are relying on this mechanism to create null entries for a subsequent for...in, they won't be there in perl. If a2p makes a split line that assigns to a list of variables that looks like (Fld1, Fld2, Fld3...) you may want to rerun a2p using the -n option mentioned above. This will let you name the fields throughout the script. If it splits to an array instead, the script is probably referring to the number of fields somewhere. The exit statement in awk doesn't necessarily exit; it goes to the END block if there is one. Awk scripts that do contortions within the END block to bypass the block under such circumstances can be simplified by removing the conditional in the END block and just exiting directly from the perl script. Perl has two kinds of array, numerically-indexed and associative. Perl associative arrays are called "hashes". Awk arrays are usually translated to hashes, but if you happen to know that the index is always going to be numeric you could change the {...} to [...]. Iteration over a hash is done using the keys() function, but iteration over an array is NOT. You might need to modify any loop that iterates over such an array. Awk starts by assuming OFMT has the value %.6g. Perl starts by assuming its equivalent, $#, to have the value %.20g. You'll want to set $# explicitly if you use the default value of OFMT. Near the top of the line loop will be the split operation that is implicit in the awk script. There are times when you can move this down past some conditionals that test the entire record so that the split is not done as often. For aesthetic reasons you may wish to change index variables from being 1-based (awk style) to 0-based (Perl style). Be sure to change all operations the variable is involved in to match. Cute comments that say "# Here is a workaround because awk is dumb" are passed through unmodified. Awk scripts are often embedded in a shell script that pipes stuff into and out of awk. Often the shell script wrapper can be incorporated into the perl script, since perl can start up pipes into and out of itself, and can do other things that awk can't do by itself. Scripts that refer to the special variables RSTART and RLENGTH can often be simplified by referring to the variables $`, $& and $', as long as they are within the scope of the pattern match that sets them. The produced perl script may have subroutines defined to deal with awk's semantics regarding getline and print. Since a2p usually picks correctness over efficiency. it is almost always possible to rewrite such code to be more efficient by discarding the semantic sugar. For efficiency, you may wish to remove the keyword from any return statement that is the last statement executed in a subroutine. A2p catches the most common case, but doesn't analyze embedded blocks for subtler cases. ARGV[0] translates to $ARGV0, but ARGV[n] translates to $ARGV[$n-1]. A loop that tries to iterate over ARGV[0] won't find it. ENVIRONMENT
A2p uses no environment variables. AUTHOR
Larry Wall <larry@wall.org> FILES
SEE ALSO
perl The perl compiler/interpreter s2p sed to perl translator DIAGNOSTICS
BUGS
It would be possible to emulate awk's behavior in selecting string versus numeric operations at run time by inspection of the operands, but it would be gross and inefficient. Besides, a2p almost always guesses right. Storage for the awk syntax tree is currently static, and can run out. perl v5.16.2 2012-08-26 A2P(1)
All times are GMT -4. The time now is 09:02 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy