using awk and printf in for loop bash

Question

How can I use awk and printf in for loop?

Here is my code

for fileName in /home/BamFiles/sample*
do
       sampleIds=${fileName##*/}

    for Bam in /home/BamFiles/sample*/*.bam
    do
        samtools idxstats $Bam | awk '{i+=$3+$4} END {printf("%s\t%d",$sampleIds Bam)}'
    done

 done

I get the the following error

 awk: fatal: not enough arguments to satisfy format string
 `%d    %s'
     ^ ran out for this one

Expected output is

  sample1  52432
  sample2  32909
  sample3  54000
  sample5  45890

Thanks

konsolebox · Accepted Answer · 2014-07-26 14:21:02Z

1

Awk can never be able to expand a shell variable. You are also trying to pass only a single argument to printf (nothing is passed for %d.

Perhaps you want it this way:

samtools idxstats "$Bam" | awk -v "file=$fileName" '{i+=$3+$4} END {printf("%s\t%d\n", file, i)}'

Note that embedding a variable's value directly to awk's code may be possible by using double-quotes but is not recommended:

samtools idxstats "$Bam" | awk "{i+=\$3+\$4} END {printf(\"%s\\t%d\", $file, i)}"

Suggestion:

shopt -s nullglob
for sample in /home/BamFiles/sample*; do
    for bam in "$sample"/*.bam; do
        samtools idxstats "$bam"
    done | awk -v sample="${sample##*/}" '{ i += $3 + $4 } END { printf("%s\t%d\n", sample, i) }'
done

Or

shopt -s nullglob
for sample in /home/BamFiles/sample*; do
    for bam in "$sample"/*.bam; do
        samtools idxstats "$bam" | \
            awk -v sample="${sample##*/}" -v bam="${bam##*/}" \
                '{ i += $3 + $4 } END { printf("%s\t%s\t%d\n", sample, bam, i) }'
    done
done

edited Jul 26, 2014 at 14:21

answered Jul 26, 2014 at 13:12

konsolebox

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3 Comments

hash Over a year ago

thanks for your answer. I was suppose to pass sampleIds to %d so I have edited it.

konsolebox Over a year ago

@hash Can you try my suggestions?

konsolebox Over a year ago

When you tried my first suggestion you probably omitted \ or added a space after it. I modified it to just run it as a line.

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