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Inserting a variable in awk script

 
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# 1  
Old 02-19-2016
Inserting a variable in awk script
I have file input.txt:
Code:
>TX1-1 Freq 55
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-2 Freq 19
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-3 Freq 17
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-4 Freq 6
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-5 Freq 6
cattctgatgaatatttgtcctttagttgttatttgt

And I am using the following ChangeID script to modify the ID (>XXXXX)
Code:
#!/bin/bash
if [ -f $1 ]
then
	file=$1
fi
pattern=$2
awk 'FNR==1{n=$pattern} /^>/ {print ">" n "-" ++c, $3;next}1' $file > New$file

So, when I enter ChangeID Input.txt Pat3, I am expecting to use the second field (Pat 3) to replace the beginning of the ID (>Pat3-XXX). Thus, the desire output file would look like this:
Code:
>Pat3-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Pat-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-5 6
cattctgatgaatatttgtcctttagttgttatttgt

But that did not work obviously. I have tried changing the AWK part of my script to
Code:
awk 'FNR==1{n=$2} /^>/ {print ">" n "-" ++c, $3;next}1' $file > New$file

But the script, of course, uses the second field on the row (Freq), outputting the following file:
Code:
>Freq-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-5 6
cattctgatgaatatttgtcctttagttgttatttgt

Any help will be greatly appreciated
# 2  
Old 02-20-2016
Making some guesses at what you were trying to do, you might want to consider this alternative script:
Code:
#!/bin/bash
if [ ! -r "$1" ]
then
	printf '%s: File not readable: "%s"\n' "${0##*/}" "$1" >&2
	exit 1
fi
pattern=${2:-Default}
awk -v n="$pattern" '/^>/ {print ">" n "-" ++c, $3;next}1' "$1" > "New$1"

With your sample data, invoking this script with:
Code:
./ChangeID input.txt Pat3

writes:
Code:
>Pat3-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-5 6
cattctgatgaatatttgtcctttagttgttatttgt

into Newinput.txt.
This User Gave Thanks to Don Cragun For This Post:
Xterra
# 3  
Old 02-20-2016
Hello Xterra,

If I understood your requirement correctly, then following may help you in same.
1st case: Let's say in case values in Input_file TX1-1 will be in increasing order then following may be helpful for same.
Code:
awk '/^>TX1/{sub("TX1","Pat3",$0);sub($2,X);print;next} 1'  Input_file

Output will be as follows.
Code:
>Pat3-1  55
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-2  19
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-3  17
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-4  6
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-5  6
cattctgatgaatatttgtcctttagttgttatttgt

2nd case: Assuming when your Input_file doesn't have values of >TX1 increasing order, then following may help you in same.
Code:
awk '/^>TX1/{sub("TX1","Pat3",$0);++c;sub(/\-.*[[:space:]]+/,"-" c" ",$0);print;next} 1'   Input_file

Output will be as follows.
Code:
>Pat3-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-5 6
cattctgatgaatatttgtcctttagttgttatttgt

Thanks,
R. Singh
# 4  
Old 02-20-2016
@Ravinder, with that approach no shell variables are passed to the awk script, which was what the OP was trying to achieve..
This User Gave Thanks to Scrutinizer For This Post:
RavinderSingh13
# 5  
Old 02-20-2016
Thanks Scrutinizer Smilie, my bad I didn't understood it completely.

Hello Xterra,

Could you please with following scripts and let me know if this helps. It has conditions like to check Input_file which is being passed to script as variable if that is really present or not and then check the existence of $2 which is pattern we need to get in output. Though suggestion provided by Don is better than this.
For case 1st: When assuming your values are in increasing order for >TX1-.
Code:
cat script1.ksh
if [[ -f $1 ]]
then
        INPUT_FILE=$1
else
        echo "Input_file passed as an argument $1 is NOT found."
        exit;
fi
if [[ -n $2 ]]
then
        PATTERN=$2
else
        echo "You haven't entered the pattern so script is exiting now."
         exit;
fi
awk -vpattern="$2" '/^>TX1/{sub("TX1",pattern,$0);sub($2,X);print;next} 1' "$INPUT_FILE"

For case 2nd: When we are assuming your >TX1- is not in increasing order, it may help.
Code:
cat script1.ksh
if [[ -f $1 ]]
then
        INPUT_FILE=$1
else
        echo "Input_file passed as an argument $1 is NOT found."
        exit;
fi
if [[ -n $2 ]]
then
        PATTERN=$2
else
         echo "You haven't entered the pattern so script is exiting now."
          exit;
fi
 
awk -vpattern="$2" '/^>TX1/{sub("TX1",pattern,$0);++c;sub(/\-.*[[:space:]]+/,"-" c" ",$0);print;next} 1' "$INPUT_FILE"

Output will be as follows in both of the above cases.
Code:
./script1.ksh file3 Pat
>Pat-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Pat-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Pat-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Pat-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Pat-5 6
cattctgatgaatatttgtcctttagttgttatttgt

Thanks,
R. Singh
Last edited by RavinderSingh13; 02-20-2016 at 04:45 AM..
This User Gave Thanks to RavinderSingh13 For This Post:
Xterra
# 6  
Old 02-20-2016
Thank you guys! Exactly what I needed
 
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