[awk] line by line processing the same file Post: 302708739

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Top Forums Shell Programming and Scripting [awk] line by line processing the same file Post 302708739 by origamisven on Tuesday 2nd of October 2012 06:20:10 AM

10-02-2012

Registered User

[awk] line by line processing the same file

Hey, not too good at this, so I only managed a clumsy and SLOW solution to my problem that needs a drastic speed up. Any ideas how I write the following in awk only?

Code is supposed to do...
For every line read column values $6, $7, $8 and do a calculation with the same column values of every other line in the same file. If conditions are met, write information out to file.

CODE:

Code:

while read line; do                                                                                     
    XI=$(echo $line | awk '{print $6}')
    YI=$(echo $line | awk '{print $7}')
    ZI=$(echo $line | awk '{print $8}')
    ATOM_TYPE=$(echo $line | awk '{print $3}')
    awk -v xi="$XI" -v yi="$YI" -v zi="$ZI" -v atom="$ATOM_TYPE" -v cutoff="$DISTCUT" '{dist=sqrt(( xi- $6)^2 + ( yi- $7)^2 + ( zi- $8)^2); if (dist <= cutoff && dist != '0') print atom, $3, dist}' sub_oxy_high >> oxy_dist_all
done < sub_oxy_high

INPUT:

Code:

ATOM   5202   C3  TB   347      47.749   6.795 193.827
ATOM   5203   C4  TB   347      46.729   7.915 193.597
ATOM   5204   O5  TB   347      47.109   9.075 193.407
ATOM   5205   O6  TB   347      45.329   7.594 193.517
...

OUTPUT:

Code:

C3 C4 9.999
C3 O5 9.999
C3 O6 9.999
...

origamisven

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LEARN ABOUT CENTOS

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).

Free Software Foundation					    Nov 3 1999								  IGAWK(1)

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igawk