It looks like you've got a FASTA format file. There are lots of modules on the CPAN to handle that file format, for example the BioPerl suite is frequently recommended. There are various nodes on this site that show the use of that module.

Other than that, as has already been said, please see How do I post a question effectively? and Short, Self-Contained, Correct Example - in this case, your question is missing representative sample input and the expected output for that input, which means that anyone wishing to help you has to make some up, and that may not be representative of your actual input. Update: I'm going to assume that this node shows representative input, despite the fact that it doesn't compile.

"How do I use the map command for this?"

No idea. :-)

"I am pretty sure I need to use the map command"

Why?

In the code below, I simplified the data so that it's easier to see what's happening. I've also jumbled it up to demonstrate the two sorts — you may not need or want either of these (biological data can be huge, so don't do any sorting unless it's absolutely necessary).

#!/usr/bin/env perl

use strict;
use warnings;

my %res;

{
    local $/ = "\n>";

    while (my $record = <DATA>) {
        chomp $record;
        $record = substr $record, 1 if $. == 1;
        $record =~ s/\s*\z//m;
        my ($id, $anno_seq) = split /\|/, $record, 2;
        push @{$res{$anno_seq}}, $id;
    }
}

print '>', join('|', (sort @{$res{$_}}), $_), "\n"
    for sort { $res{$a}[0] cmp $res{$b}[0] } keys %res;

__DATA__
>id7|anno2
GHI
>id1|anno1
ABC
>id6|anno1
ABC
>id4|anno2
GHI
>id2|anno3
DEF
>id3|anno1
ABC
>id5|anno1
ABC
[download]

Output:

>id1|id3|id5|id6|anno1
ABC
>id2|anno3
DEF
>id4|id7|anno2
GHI
[download]

#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11144847
use warnings;

my %res;
/(id\d+)(.*)/s and push @{ $res{$2} }, $1 for split />/, join '', <DAT
+A>;
for ( sort keys %res )
  {
  local $" = '|';
  print ">@{$res{$_}}$_";
  }

__DATA__
>id1|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id2|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id4|Q51487|P-474-4|86-98,113-126,297-310,322-335 alt
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id5|Q51487|P-474-4|86-98,113-126,297-310,322-335 alt
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
[download]

Outputs:

>id1|id2|id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id4|id5|Q51487|P-474-4|86-98,113-126,297-310,322-335 alt
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALEc>
[download]

Suggestions:

• get an account here, so you can edit and fix your postings
• provide us with an SSCCE with clear input and expected output

Yes, probably it was not well-written. Imagine this script:


use strict;
use warnings;

my %res;
my $id='';
my $rest='';
my $seq='';
while (<DATA>) 
{
    chomp;
    if($_=~/^>(.*?)\|(.*)/)
    {
        $id=$1;
        $rest=$2;
        $seq=<DATA>;
        chomp $seq;
    }
}

_DATA_
>id1|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id2|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
[download]


and I want to go to:


>id1|id2|id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
[download]


And I wonder if I can use some of Perl's data structures, or the map command?

As usual, TIMTOWTDI. However, keeping your initial code structure for better or worse:

use strict;
use warnings;

use Test::More tests => 1;

my $want = <<EOT;
>id1|id2|id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
EOT

my %res;

while (<DATA>) {
    if (/^>(.*?)\|(.*)/s) {
        my $id   = $1;
        my $rest = $2;
        if (exists $res{$rest}) {
            $res{$rest}{keys} .= "|$id";
        } else {
            my $seq = <DATA>;
            $res{$rest} = {
                keys => ">$id",
                seq => $seq,
            }
        }
    }
}

my ($k) = keys %res; # You would loop over all keys is your real prog
my $have = "$res{$k}{keys}|$k$res{$k}{seq}";
is $have, $want;

__DATA__
>id1|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id2|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
>id3|Q51487|P-474-4|86-98,113-126,297-310,322-335
CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE
[download]

---

🦛

> _DATA_

I can tell immediately that this doesn't run! 👎

You should check before posting, that's the "Correct" part in SSCCE!

And it's not clear to me which part has to be unique...

This

|Q51487|P-474-4|86-98,113-126,297-310,322-335

or this

CSLIPDYQRPEAPVAAAYPQGQAYGQNTGAAAVPAADIGWREFFRDPQLQQLIGVALE

or both.

This has not much to do with map, a HoA = Hash of Arrays with unique keys (well which one?) is enough.

Or probably a HoHoA depending on your perception of unique.

And of course also depending on your desired output order.

Please show more effort!

Cheers Rolf
_{(addicted to the Perl Programming Language :)
Wikisyntax for the Monastery}

I had this older script that was doing something similar, but with two values separated by tab:


use strict;
use warnings;

my %res;
while (<>) 
{
    chomp;
    my ( $name, $rest ) = split /\t/;
    push @{ $res{$name} }, $rest;
}
for ( sort keys %res ) 
{
    print "$_:", join( ",", @{ $res{$_} } );
    print "\n";
}
[download]


but I do not know how to adapt it.

The map statement is just a short-hand way of writing a simple "for" loop.
ALL map's can be expressed as "for" (foreach) loops.
Perl generates the same code for a "map" as the equivalent "foreach" loop.

map{} is not your issue.

I think looking at Bio::Perl will lead to some suggestions for you. There are many routines optimized for the FASTA format.

Perl generates the same code for a "map" as the equivalent "foreach" loop.

wrong

Would certainly enjoy being educated. I probably should have said "similar". A map is a looping statement.