Print for loop input filename on piped awk output

Question

I wish to print $fname on each line of awk the ouput for the following:

for fname in $(ls *.bam | cut -c -9 | uniq)
    do
    echo $fname
    samtools depth  -a "$fname".bam | awk '{sum+=$3} END {print "Average = ", sum/NR}' >> mean.depth
    done

Current output:

$ less mean.depth  
    Average =  5.40089
    Average =  4.68387

Desired output:

$ less mean.depth  
    FILENAME1 Average =  5.40089
    FILENAME2 Average =  4.68387

So that the output mean depths are traceable. I've tried FILENAME and all sorts of things but not succeeding. Thanks!

since awk is acting upon stdin, FILENAME won't work... pass the shell variable containing filename, see https://stackoverflow.com/questions/19075671/how-do-i-use-shell-variables-in-an-awk-script — Sundeep, Nov 03 '17 at 08:50
@GMK: Since you found a solution, you should post it as an answer to your question — Thor, Nov 03 '17 at 10:06

GMK · Accepted Answer · 2017-11-03T10:42:30.297

0

SOLUTION

adapted from this answer

Define shell variable $fname with awk -v var=, then print it with END {print var

samtools depth  -a "$fname".bam | awk -v var=$fname '{sum+=$3} END {print var, " = ", sum/NR}' >> mean.depth

edited Nov 03 '17 at 10:42

answered Nov 03 '17 at 10:25

GMK

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Print for loop input filename on piped awk output

1 Answers1