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Full Discussion: Looping through pairs of files with awk
Top Forums Shell Programming and Scripting Looping through pairs of files with awk Post 302828171 by newbie83 on Tuesday 2nd of July 2013 01:17:22 AM
Old 07-02-2013
Looping through pairs of files with awk
Hi all,

please help me construct the command. i want to loop through all files named bam* and bed*. My awk works for a particular pair but there are too many pairs to do manually.

I have generated multiple files in a folder in a given pattern. The files are named like

Code:
bam_fixed1.bam
bed_fixed1.bed
bam_fixed2.bam
bed_fixed2.bed
....
.....

so that every bam file is paired with a bed file. The fixed portion of the filename is the same for a particular pair of bam and bed.

I want to construct an awk command which acts on a bam and its particular bed pair..

what I want to do is for all pairs

Code:
awk 'NR == FNR { commands }'  bam_fixed1.bam bed_fixed1.bed > out_fixed1.txt

awk 'NR == FNR { commands }' bam_fixed2.bam bed_fixed2.bed > out_fixed2.txt

...

If there was only 1 file I can use a for loop like

Code:
for f in bam_*.bam
do
  commands with $f
done

How do I do this for multiple files and corresponding pairs?
 

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LEARN ABOUT REDHAT

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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