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Top Forums Shell Programming and Scripting Challenging Awk array problem Post 302423803 by alister on Saturday 22nd of May 2010 01:19:38 PM
Old 05-22-2010
If you prefer it that way, sure.

Code:
awk -f dna.awk f2='file2' file1

Where dna.awk contains:
Code:
{chr=$6; min=$7; max=$8; s=$11" "$12" "$13; getline < f2; if (chr==$4 && $5>=min && $5<=max) print $0, s;}

If you still have problems, copy-paste the commands exactly as you ran them and the error messages exactly as you see them. Perhaps that will enable someone with experience dealing with unix tools on windows to help out.

Alister

---------- Post updated at 01:19 PM ---------- Previous update was at 01:14 PM ----------

Or, simpler still, you can put it into a shell script:

Code:
#!/bin/sh

awk '{chr=$6; min=$7; max=$8; s=$11" "$12" "$13; getline < f2; if (chr==$4 && $5>=min && $5<=max) print $0, s;}' f2="$2" "$1"

Assuming the shell script file is named dna.sh, exists in the current directory, and is made executable, it can be run thusly:
Code:
$ ./dna.sh file1 file2
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074 chr1  3000072  TTTATCGTCATCGTC L1_Mur2 LINE L1

Or, if not an executable file:
Code:
$ sh dna.sh file1 file2
4|17999 - gi|149361523|ref|NC_000074.5|NC_000074 chr1  3000072  TTTATCGTCATCGTC L1_Mur2 LINE L1

This User Gave Thanks to alister For This Post:
 

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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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