Shell Programming and Scripting

cat File.txt
>H1_A1_A2_A3_A4_ID1_A5
A:B:C:S:E:E:K
>H2_A1_A2_A3_ID2_A5
A:B:C:S:E:E:K
D:E:G
>H3_A1_A2_A3_ID5_A5
A:B:S:R:E:K
D:E

cat comments.txt
ID1;NT001;QTR231
ID2;NT002;QTR251
ID3;NT011;QTR331
ID4;NT022;QTR311
ID5;NT023;QTR551

>H1_A1_A2_A3_A4_ID1_A5 ID1 NT001 QTR231
A:B:C:S:E:E:K
>H2_A1_A2_A3_ID2_A5 ID2 NT002 QTR251
A:B:C:S:E:E:K
D:E:G
>H3_A1_A2_A3_ID5_A5 ID5 NT023 QTR551
A:B:S:R:E:K
D:E

#! /bin/bash 

grep ">" $1 | awk -F_ '{print $(NF-1)}' > IDtag.tmp

while read ID
do
    COMMENT=`grep "$ID" $2 | awk -F ";" '{$1="";print}' `
    HEADER=`grep "$ID" $1`
    #DATA=`grep -v "$ID" $1`
    echo $HEADER $COMMENT
    #echo $DATA
    
done < IDtag.tmp

rm IDtag.tmp

awk 'NR==FNR{gsub(";"," ");a[$1]=$0;next}/^>/{x=$0;sub(".*_ID","ID",x);sub("_.*","",x);$0=$0" "a[x]}1' comments.txt File.txt

gawk -F";" 'NR==FNR{a[$1]=$1" "$2" "$3;next} {for(ID in a){if($0~ID)print $0, a[ID]}} $0!~">.*"{print $0}' comments.txt File.txt

$ cat infile
>H1_A1_A2_A3_A4_ID1_A5
A:B:C:S:E:E:K
>H2_A1_A2_A3_ID2_A5
A:B:C:S:E:E:K
D:E:G
>H3_A1_A2_A3_ID5_A5
A:B:S:R:E:K
D:E
$ cat script.pl
use warnings;
use strict;
use autodie;

my %comments;

@ARGV == 2 or die qq(Usage: perl $0 file comments\n);

open my $file_h, "<", $ARGV[0];
open my $comments_h, "<", $ARGV[1];

while ( <$comments_h> ) {
        chomp;
        next if /^\s*$/ || ! /;/;
        my @f = split /;/;
        $comments{ $f[0] } = join " ", @f;
}

while ( <$file_h> ) {
        chomp;
        if ( index( $_, ">" ) == 0 ) {
                my @f = split /_/;
                printf "%s\n", $_ . " " . $comments{ $f[$#f - 1] } || "";
                next;
        }

        printf "%s\n", $_;
}
$ perl script.pl infile comments 
>H1_A1_A2_A3_A4_ID1_A5 ID1 NT001 QTR231
A:B:C:S:E:E:K
>H2_A1_A2_A3_ID2_A5 ID2 NT002 QTR251
A:B:C:S:E:E:K
D:E:G
>H3_A1_A2_A3_ID5_A5 ID5 NT023 QTR551
A:B:S:R:E:K
D:E