How to add header name to all annotation lines

Question

[Sam]

Hi there,

how to append the header line (chromosome or scaffold) to the end of each annotation.

---

Input:

@Chr1

54584 54773 100 1.9 98

55019 55105 22 3.9 22

---

@Chr2

2226 2261 18 1.9 19

4211 4259 26 1.9 25

4426 4468 22 2 22

---

@utg7294

919 1455 36 15 36

919 1455 71 7.5 72

4872 4913 22 1.9 22

---

Expected output

54584 54773 100 1.9 98 @Chr1

55019 55105 22 3.9 22 @Chr1

---

2226 2261 18 1.9 19 @Chr2

4211 4259 26 1.9 25 @Chr2

4426 4468 22 2 22 @Chr2

---

919 1455 36 15 36 @utg7294

919 1455 71 7.5 72 @utg7294

4872 4913 22 1.9 22 @utg7294

It must be simple as search line has '@', if so append that header to end until it finds another '@'. But I couldn't find an exact script.

Thanks for your help. Sam

Answer 1

[ATpoint]

DELIMITER="\t"
awk NF your.file | \
  while read p; do
  if [[ $p == @* ]]; then 
    APPEND=$p
    continue
      fi
  if [[ $p != @* ]]; then 
    echo -e ${p}${DELIMITER}${APPEND}
    fi
  done < /dev/stdin

Change DELIMITER in line 1 according to the delimiter present in your file. Here is is tab.

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Also, for the future, please use the code option (101010) in the formatting bar to indicate code and example data.

Answer 2

[JC]

Perl:

#!/usr/bin/perl

use strict;
use warnings;

my $head = '';
while (<>) {
    chomp;
    if (/^(@.+)/) { $head = $1; }
    else { print "$_\t$head\n"; }
}

Run as perl addheader.pl < INPUT > OUPUT