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Full Discussion: Counts not matching in file
Top Forums Shell Programming and Scripting Counts not matching in file Post 302960234 by cmccabe on Thursday 12th of November 2015 02:59:26 PM
Old 11-12-2015
Counts not matching in file

I can not figure out why there are 56,548 unique entries in test.bed. However, perl and awk see only 56,543 and that # is what my analysis see's as well. What happened to the 5 missing? Thank you Smilie.

The file is attached as well.

Code:
cmccabe@DTV-A5211QLM:~/Desktop/NGS/bed/bedtools$wc -l test.bed
56548 test.bed

cmccabe@DTV-A5211QLM:~/Desktop/NGS/bed/bedtools$ perl -nae '$seen{$F[3]}++;
    END{
        print "There are ", scalar keys %seen, " unique fourth fields\n";
    }' test.bed
There are 56543 unique fourth fields

cmccabe@DTV-A5211QLM:~/Desktop/NGS/bed/bedtools$ awk '$4!=d{c++;d=$4}END{print c}' test.bed
56543

 

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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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