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Full Discussion: Short program to select lines from a file based on a second file
Top Forums Shell Programming and Scripting Short program to select lines from a file based on a second file Post 302732929 by Homa on Monday 19th of November 2012 11:19:27 AM
Old 11-19-2012
Short program to select lines from a file based on a second file
Hello,

I use UBUNTU 12.04.

I want to write a short program using awk to select some lines in a file based on a second file.

My first file has this format with about 400,000 lines and 47 fields:
SNP1 1 12.1
SNP2 1 13.2
SNP3 1 45.2
SNP4 1 23.4
My second file has this format:
SNP2
SNP3
SNP5
SNP10

I want to have an output like this:
SNP2 1 13.2
SNP3 1 45.2
SNP5 1 23.2
SNP10 1 45.2
That is I have basically the first file but only with the SNPs that exist in the second file, it is important that it gives me back the whole row.

I wrote a code as following but it does not work:

Code:
BEGIN{
OFS=ORS=" "
}
{
if(FILENAME==ARGV[1]){SNP_name[$1]=FNR}
if(FILENAME==ARGV[2]){
if($1 in SNP_name){sel[SNP_name[$1]]=$1}
{
print $0 > test
}

Thank you for any help.
 

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LEARN ABOUT OPENSOLARIS

igawk

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).

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +--------------------+-----------------+
       |  ATTRIBUTE TYPE    | ATTRIBUTE VALUE |
       +--------------------+-----------------+
       |Availability	    | SUNWgawk	      |
       +--------------------+-----------------+
       |Interface Stability | Volatile	      |
       +--------------------+-----------------+
NOTES

       Source for gawk is available on http://opensolaris.org.

Free Software Foundation					    Nov 3 1999								  IGAWK(1)
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