Sponsored Content
Top Forums Shell Programming and Scripting awk to change value in field according to another Post 303027171 by cmccabe on Monday 10th of December 2018 10:39:02 AM
Old 12-10-2018
I the original code below the bold is the static or the file that is always used. The italics output is set by prefand $file is the underlined portion and would be dependent on each .txt file in the directory.

Quote:
I also note that the exon.sh can't be the script that I supplied in post #11. That script didn't look at any of its operands; it only used the presence of one or more operands as a flag to enable debugging printouts. I will assume that you removed the debugging printf statements and the d variable and are using the two operands you are passing to exon.sh as the two filenames processed by that script.
Since one of the operands will never change and the other is set by the for loop are you saying (sorry for my confusion).I added comments as well. Thank you Smilie.

Code:
#!/bin/sh
awk -v d=$# '    (the d=$# is removed because the files are dependent on the for loop)
BEGIN {	FS = "[\t_]"
	OFS = "\t"
}
FNR == NR {
	m[$1, $4, ++c[$1, $4]] = $2 + 0
	M[$1, $4, c[$1, $4]] = $3 + 0
	if(d) printf("m[%s,%s,%d]=%s,M[%s,%s,%d]=%s\n",
		$1, $4, c[$1, $4], m[$1, $4, c[$1, $4]],
		$1, $4, c[$1, $4], M[$1, $4, c[$1, $4]])
	next
}
{	#if(d) printf("FNR=%d:\"%s\"\n",FNR,$0) (remove this line as it assumes d is typed in)
	for(i = 1; i <= c[$1, $4]; i++) {
		if(d) printf("m[%d]=%d,M[%d]=%d,$2=%d\n",
			i, m[$1, $4, i],
			i, M[$1, $4, i],
			$2)
		if(m[$1, $4, i] <= $2 && $2 <= M[$1, $4, i]) {
			$5 = "exon"
			break
		} else {if(m[$1, $4, i] > $2 + 0) {
				if(m[$1, $4, i] - 10 <= $2 + 0) {
					$5 = "splicing"
					break
				} else {$5 = "intron"
					break
				}
		}
	}
}
	if(i > c[$1, $4])
		$5 = "intron"
}
1' all_cdsV2 00-0000low > 00-0000_filter


Last edited by cmccabe; 12-10-2018 at 04:05 PM.. Reason: corrected typo
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

change field content awk

I have a line like this: I want to move HTTP/1.1 200 OK to the next line and put a blank line between the two lines i.e. How can i get it using awk? Thanks in advance (2 Replies)
Discussion started by: littleboyblu
2 Replies

2. Shell Programming and Scripting

dynamically change awk Field Separator FS

Hi All, I was wondering if anyone knew how to dynamically change the FS in awk to accept vairiable containing a field separator. the current code is as below and does not work when i introduce the dynamic FS change :-( validate_source_file() { source_file=$1 ... (2 Replies)
Discussion started by: satnamx
2 Replies

3. Shell Programming and Scripting

awk,cut fields by change field format

Hi Everyone, # cat 1.txt 1321631,77770132976455,19,20091001011859,20091001011907 1321631,77770132976455,19,20091001011859,20091001011907 1321631,77770132976455,19,20091001011859,20091001011907 # cat 1.txt | awk -F, '{OFS=",";print $1,$3,$4,$5}' 1321631,19,20091001011859,20091001011907... (7 Replies)
Discussion started by: jimmy_y
7 Replies

4. Shell Programming and Scripting

awk, comma as field separator and text inside double quotes as a field.

Hi, all I need to get fields in a line that are separated by commas, some of the fields are enclosed with double quotes, and they are supposed to be treated as a single field even if there are commas inside the quotes. sample input: for this line, 5 fields are supposed to be extracted, they... (8 Replies)
Discussion started by: kevintse
8 Replies

5. Shell Programming and Scripting

AWK: Pattern match between 2 files, then compare a field in file1 as > or < field in file2

First, thanks for the help in previous posts... couldn't have gotten where I am now without it! So here is what I have, I use AWK to match $1 and $2 as 1 string in file1 to $1 and $2 as 1 string in file2. Now I'm wondering if I can extend this AWK command to incorporate the following: If $1... (4 Replies)
Discussion started by: right_coaster
4 Replies

6. Shell Programming and Scripting

awk or sed? change field conditional on key match

Hi. I'd appreciate if I can get some direction in this issue to get me going. Datafile1: -About 4000 records, I have to update field#4 in selected records based on a match in the key field (Field#1). -Field #1 is the key field (servername) . # of Fields may vary # comment server1 bbb ccc... (2 Replies)
Discussion started by: RascalHoudi
2 Replies

7. UNIX for Dummies Questions & Answers

change field separator only from nth field until NF

Hi ! input: 111|222|333|aaa|bbb|ccc 999|888|777|nnn|kkk 444|666|555|eee|ttt|ooo|ppp With awk, I am trying to change the FS "|" to "; " only from the 4th field until the end (the number of fields vary between records). In order to get: 111|222|333|aaa; bbb; ccc 999|888|777|nnn; kkk... (1 Reply)
Discussion started by: beca123456
1 Replies

8. Shell Programming and Scripting

awk :how to change delimiter without giving all field name

Hi Experts, i need to change delimiter from tab to "," sample test file cat test A0000368 A29938511 072569352 5 Any 2 for £1.00 BUTCHERS|CAT FOOD|400G Sep 12 2012 12:00AM Jan 5 2014 11:59PM Sep 7 2012 12:00AM M 2.000 group 5 ... (2 Replies)
Discussion started by: Lakshman_Gupta
2 Replies

9. Shell Programming and Scripting

awk to change value of field using multiple conditions

In the below awk in the first step I default Classification NF-1 to VUS. Next, I am trying to change the value of Classification (NF) to whatever CLINSIG (NF-1) is. If there is only one condition everything works great, but if there are two conditions it does not work. Is the syntax used... (4 Replies)
Discussion started by: cmccabe
4 Replies

10. Shell Programming and Scripting

awk to change contents of field based on condition in same file

In the awk below I am trying to copy the entire contents of $6 there may be multiple values seperated by a ;, to $8, if $8 is . (lines 1 and 3 are examples). If that condition $8 is not . (line2 is an example) then that line is skipped and printed as is. The awk does execute but prints the output... (3 Replies)
Discussion started by: cmccabe
3 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 v5.12.4 2011-06-01 A2P(1)
All times are GMT -4. The time now is 08:22 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy