awk to add header to output file

Question

I am trying to filter a file_to_filter by using another filter_file, which is just a list of strings in $1. I think I am close but can not seem to include the header row in the output. The file_to_filter is tab delimited as well. Thank you :).

file_to_filter

Chr Start   End Ref Alt Func.refGene    Gene.refGene
chr1    160098543   160098543   G   A   exonic  ATP1A2
chr1    172410967   172410967   G   A   exonic  PIGC

filter_file

PIGC

desired output (header included)

Chr Start   End Ref Alt Func.refGene    Gene.refGene
chr1    172410967   172410967   G   A   exonic  PIGC

awk with current output (header not included)

awk -F'\t' 'NR==1{A[$1];next}$7 in A' file test

chr1    172410967   172410967   G   A   exonic  PIGC

Ed Morton · Accepted Answer · 2016-10-03 16:48:56Z

2

Assuming your fields really are tab-separated:

awk -F'\t' 'NR==FNR{tgts[$1]; next} (FNR==1) || ($7 in tgts)' filter_file file_to_filter

To start learning awk, read the book Effective Awk Programing, 4th Edition, by Arnold Robbins.

answered Oct 3, 2016 at 16:48

Ed Morton

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