Shell Programming and Scripting

DB|QZX3  140  165  RT_2   VgGIGvGVR
DB|QZX3  155  182  UT_1   rlgslqqLaIvlGiFT
DB|QZX3  345  362  RT_1   GRKpllligS
DB|ZXK6  174  199  RT_2  IstvtvptYlgEiatvkaR
DB|ZXK6  189  216  UT_1    algtiyqLfLviGiLF
DB|AZ264  15  17    RT_2  getapvYlaEmspasiR
DB|A1Z8N1  457  474  RT_1  GGPLIEYLGRRntilatA
DB|A1Z8N1  499  524 RT_2  LaGFCvGIaslsqpevR
DB|A1Z8N1  690  706  RT_1  GIVLIDKillyv.S
DB|A3M0N3  133  158  RT_2  LaGLGvGLiR
DB|A3M0N3  334  351  RT_1  GIGRRklllggS

ID                  RT_1                                 RT_2                                        UT1
DB|QZX3        G R K p l l l i g S                    V g G I G v G V R                             r l g s l q q L a I v l G i F T
DB|ZXK6                                               I s t v t v p t Y l g E i a t v k a R         a l g t i y q L f L v i G i L F
DB|AZ264                                              g e t a p v Y l a E m s p a s i R
DB|A1Z8N1      G G P L I E Y L G R R n t i l a t A
DB|A1Z8N1      G I V L I D K i l l y v . S
DB|A3M0N3      G I G R R k l l l g g S                L a G L G v G L i R

RT1
RT2
RT_1
RT_2
UT1

#!/usr/bin/perl
use strict;
use warnings;

open my $input, "<", "$ARGV[0]" or die "cannot open file: $ARGV[0]";

my %output;
while (my $line = <$input>) {
  chomp $line;
  my @F = split / +/, $line;
  $output{$F[0]} = " " x 120 if !$output{$F[0]};
  substr($output{$F[0]}, 0, 40) = sprintf "%-40s", join " ", split //, $F[4] if $F[3] eq "RT_1";
  substr($output{$F[0]}, 40, 40) = sprintf "%-40s", join " ", split //, $F[4] if $F[3] eq "RT_2";
  substr($output{$F[0]}, 80, 40) = sprintf "%-40s", join " ", split //, $F[4] if $F[3] eq "UT_1";
}

print "ID" . " " x 18 . "RT_1" . " " x 34 . "RT_2" . " " x 41 . "UT_1\n";
foreach my $id (keys %output) {
  printf "%-15s%s\n", $id, $output{$id};
}

./script.pl input

awk     '       {LN[$1]; HD[$4]; gsub (/./, "& ", $5); MX[$1,$4]=$5}
         END    {FMT="%-35s"
                                printf FMT, "ID"; for (i in HD) printf FMT, i; print "";
                 for (j in LN) {printf FMT, j;    for (i in HD) printf FMT, MX[j,i]; print ""}
                }
        ' file
ID                                 UT_1                               RT_1                               RT_2                               
DB|A1Z8N1                                                             G I V L I D K i l l y v . S        L a G F C v G I a s l s q p e v R  
DB|AZ264                                                                                                 g e t a p v Y l a E m s p a s i R  
DB|A3M0N3                                                             G I G R R k l l l g g S            L a G L G v G L i R                
DB|QZX3                            r l g s l q q L a I v l G i F T    G R K p l l l i g S                V g G I G v G V R                  
DB|ZXK6                            a l g t i y q L f L v i G i L F                                       I s t v t v p t Y l g E i a t v k a R