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Top Forums UNIX for Beginners Questions & Answers awk to add +1 to value based on condition in input Post 303035089 by cmccabe on Tuesday 14th of May 2019 01:37:03 PM
Old 05-14-2019
awk to add +1 to value based on condition in input

In the awk below I am trying to add a | that will adjust $2 in the ouput by adding +1 if the original value from file that was used in $3 had a - in it. Line 3 of file is an example of this. In my current awk I just subtract one but I am not sure how to only apply this to those values without a -. In my actual data there may be hundreds of lines but always the same format. Thank you Smilie.


file
Code:
2019 NGS-A Gene and Chromosomal Position List,,,,
Gene Symbol,HGNC ID,Transcript Number,Chromosomal Position/Interval ,Required (Exome and Genome Labs)
VPS13B,HGNC:2183,NM_017890.4,chr8 100493900-100493909,yes
VPS33B,HGNC:12712,NM_018668.4,chr15 91543131,

current
Code:
chr8	100493899	100493909	VPS13B
chr15	91543130	91543131	VPS33B

desired
Code:
chr8	100493900	100493909	VPS13B
chr15	91543130	91543131	VPS33B

awk
Code:
awk -F, 'FNR > 2 {for(i=1;i<=NF;i++){if($i~/^chr/){a=$i}} print a,$1}' file | awk -F'[ :-]' 'NF==3{$4=$3;$3=$2} {$1=$1} 1' OFS='\t' | awk -F'\t' '{print $1,$2-1,$3,$4}' OFS="\t" out

 

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IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
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