#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my $dir = '.';
opendir(my $dh, $dir);

for (readdir $dh) {
    next unless /^(.+?)\.fasta/;
    my ($id_path, $fasta_path) = ("$dir/$1.txt", "$dir/$_");
    next unless -e $id_path;
    my %ids = map +($_ => 1), split ' ',
              do { local $/; open my $fh, '<', $id_path; <$fh>; };

    {
        open my $fh, '<', $fasta_path;
        local $/ = '>';

        while (<$fh>) {
            chomp;

            if (/\A[^|]+\|([^)]+)/) {
                print { _get_out_fh($dir, $1) } "$/$_" if $ids{$1};
            }
        }
    }
}

_close_all_out_fhs();
closedir $dh;

{
    my %out_fh_for;

    sub _get_out_fh {
        my ($dir, $id) = @_;

        unless (exists $out_fh_for{$id}) {
            open $out_fh_for{$id}, '>', "$dir/$id.fasta";
        }

        return $out_fh_for{$id};
    }

    sub _close_all_out_fhs {
        close $_ for values %out_fh_for;

        return;
    }
}

##</code><code>##

ken@titan ~/tmp/pm_11145943
$ ls -l
total 8
-rwxr-xr-x 1 ken None 976 Aug  5 08:26 fasta_munge.pl
-rw-r--r-- 1 ken None 257 Aug  5 08:28 one.fasta
-rw-r--r-- 1 ken None  23 Aug  5 05:32 one.txt
-rw-r--r-- 1 ken None 402 Aug  5 08:28 two.fasta
-rw-r--r-- 1 ken None  23 Aug  5 05:35 two.txt

ken@titan ~/tmp/pm_11145943
$ cat one.fasta
>one:VFG000033(gb|WP_002208793)
PGRTPGVERVAHRDDDEHSWHLYAIRIHPQAPLKCDDFIVRMTENGIGCSVHYVPLHLQP
YWRDRYGLTPDMYPHSQAAFEGMASLPIYSRMTDADVQRVIASVRQLLRP
>one:VFG000036(gb|NP_490509)
ALLISLMALGVKAGDEVITTSFTFVATAEVIALLGAKPVFVDVEPDTCNIKVSEIEAKIT
PRTKAIIPVSLYGQCGDMDEV

ken@titan ~/tmp/pm_11145943
$ cat one.txt
WP_002208793
NP_490509

ken@titan ~/tmp/pm_11145943
$ cat two.fasta
>two:VFG000033(gb|WP_002208793)
PGRTPGVERVAHRDDDEHSWHLYAIRIHPQAPLKCDDFIVRMTENGIGCSVHYVPLHLQP
YWRDRYGLTPDMYPHSQAAFEGMASLPIYSRMTDADVQRVIASVRQLLRP
>two:VFG000032(gb|WP_002208792)
PGRTPGVERVAHRDDDEHSWHLYAIRIHPQAPLKCDDFIVRMTENGIGCSVHYVPLHLQP
YWRDRYGLTPDMYPHSQAAFEGMASLPIYSRMTDADVQRVIASVRQLLRP
>two:VFG000036(gb|NP_490509)
ALLISLMALGVKAGDEVITTSFTFVATAEVIALLGAKPVFVDVEPDTCNIKVSEIEAKIT
PRTKAIIPVSLYGQCGDMDEV

ken@titan ~/tmp/pm_11145943
$ cat two.txt
WP_002208792
NP_490509

ken@titan ~/tmp/pm_11145943
$ ./fasta_munge.pl

ken@titan ~/tmp/pm_11145943
$ ls -l
total 11
-rwxr-xr-x 1 ken None 976 Aug  5 08:26 fasta_munge.pl
-rw-r--r-- 1 ken None 224 Aug  5 08:31 NP_490509.fasta
-rw-r--r-- 1 ken None 257 Aug  5 08:28 one.fasta
-rw-r--r-- 1 ken None  23 Aug  5 05:32 one.txt
-rw-r--r-- 1 ken None 402 Aug  5 08:28 two.fasta
-rw-r--r-- 1 ken None  23 Aug  5 05:35 two.txt
-rw-r--r-- 1 ken None 145 Aug  5 08:31 WP_002208792.fasta
-rw-r--r-- 1 ken None 145 Aug  5 08:31 WP_002208793.fasta

ken@titan ~/tmp/pm_11145943
$ cat NP_490509.fasta
>one:VFG000036(gb|NP_490509)
ALLISLMALGVKAGDEVITTSFTFVATAEVIALLGAKPVFVDVEPDTCNIKVSEIEAKIT
PRTKAIIPVSLYGQCGDMDEV
>two:VFG000036(gb|NP_490509)
ALLISLMALGVKAGDEVITTSFTFVATAEVIALLGAKPVFVDVEPDTCNIKVSEIEAKIT
PRTKAIIPVSLYGQCGDMDEV

ken@titan ~/tmp/pm_11145943
$ cat WP_002208792.fasta
>two:VFG000032(gb|WP_002208792)
PGRTPGVERVAHRDDDEHSWHLYAIRIHPQAPLKCDDFIVRMTENGIGCSVHYVPLHLQP
YWRDRYGLTPDMYPHSQAAFEGMASLPIYSRMTDADVQRVIASVRQLLRP

ken@titan ~/tmp/pm_11145943
$ cat WP_002208793.fasta
>one:VFG000033(gb|WP_002208793)
PGRTPGVERVAHRDDDEHSWHLYAIRIHPQAPLKCDDFIVRMTENGIGCSVHYVPLHLQP
YWRDRYGLTPDMYPHSQAAFEGMASLPIYSRMTDADVQRVIASVRQLLRP

ken@titan ~/tmp/pm_11145943
$