I think Bio::SeqIO from bioperl is probably still the recommended solution rather than rolling your own parser. That aside you’re missing parens on open when you create your output file so it’s not parsing the way you intend and you may not be seeing errors from there if you do have problems. Using the three arg open and parens would be better/current best practice.

my $outfile = qq{$path/$name.faa};
open( my $out_fh, q{>}, $outfile ) or die qq{problem writing to ‘$outf
+ile’: $!};
[download]

you’re missing parens on open when you create your output file so it’s not parsing the way you intend

This isn't wrong but equally the parens are not needed if or is used for control flow instead of ||. All three of these work (my preference in the comments)

open( my $out_fh, q{>}, $outfile ) || die qq{problem writing to '$outf
+ile': $!}; # OK
open( my $out_fh, q{>}, $outfile ) or die qq{problem writing to '$outf
+ile': $!}; # Better
open my $out_fh, q{>}, $outfile or die qq{problem writing to '$outfile
+': $!};    # Best
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The last of these is an idiom I use all the time (albeit with actual quotation marks rather than q/qq). I find that absence of unnecessary punctuation makes for clearer reading but recognise that not everyone sees it the same way. There is also autodie if you don't want or need to write your own error messages.

All the rest of Fletch's advice is spot on. I'd also point you (joluito) to the Basic debugging checklist for help in finding out where things are going wrong.

---

🦛

I agree with hippo's choice, but... To paraphrase the introduction to the book "Perl Best Practices": The style is not very important. What is important is that you chose one that works for you and always use it.
Bill

G'day joluito,

Welcome to the Monastery.

Yes, some dummy input and output files would have probably been useful. You should keep these small but still representative of your real data.

I see a variety of comments on your code. I won't revisit these but I will make two points:

• When you change a special variable, such as $/, you should localise it and restrict the change to the smallest possible scope. See perlvar and local.
• Avoid reading all data into an array; then reading it all again from that array. There are occasions when this is useful, but generally it isn't: this is particularly true with biological data which, as I'm sure you're aware, can be huge. Reading and processing data one piece at a time with, for example, while and for loops, will reduce CPU cycles, memory requirements, and the overall time your program takes to run.

The following code, fasta_munge.pl, shows how I might have handled your requirements.

#!/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;
    }
}
[download]

I put together some dummy data for testing. Here's a full run with all the details.

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
$
[download]

Hi Ken,

Thank you very much for your help!

I totally agree with you! But in this case, since this particular data is not too big to handle easily, I didn't care very much about computational requirements... my fault.

The rude Anonymous person nailed it about changing the field separator.

Here's is the FUNCTIONAL code (may indentation not be that good, and the code not obfuscated enough as to win a contest...but we need it to be mantained by different people, some of who are new to programming).

#!usr/bin/perl -w
use strict;
use Getopt::Long;

#usage example: perl /path_to_script/bay_seqret.pl -p /path_to_lists -
+f /path_to_fasta/FASTA_file.faa

my ($path, $fasta);
GetOptions(
    'path=s'          => \$path,
    'fasta=s'          => \$fasta,
    );
chdir $path or die "ERROR: Unable to enter $path: $!\n";
opendir (TEMP , ".");
my @files = readdir (TEMP);
closedir TEMP;
my $name;
my $found=0;
my $totalist=0;
$/ = "\>";###CHANGED HERE TO SPLIT FASTA by ">"
open (INFILE, "$path/$fasta") || die ("cannot open input file");
chomp(my @data = <INFILE>);
print"@data\n";
$/ = "\n";####"REGENERATED" HERE NOT TO INTERFERE WITH THE REST OF THE
+ DATA PROCESSING
for my $file (@files) {
    if($file=~/(\w+)\.txt/){
        $name = "$1";
        print"Lista: $path/$name.txt\n";
        open (INFILE2, "$path/$name.txt") || die ("cannot open input f
+ile");
        chomp(my @lista = <INFILE2>);
        open  OUT,'>'."$path/$name.out" or die "ERROR: Unable to open 
+$file $!\n";
        foreach my $li (@lista){
            chomp $li;
            print"$li\n";
            $totalist++;
            for(@data){
                if(/$li/){
                    $found++;        
                    print ">"."$_\n"; 
                    print OUT ">"."$_\n";
                }
            }
        }
        print "For $name we found $found of a total $totalist\n";
    }
}
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Never mind any of the following. I didn't notice after reading your description that you're setting new output names for new files over and over.

open  OUT,'>'."$path/$name.out" or die "ERROR: Unable to open $file $!
+\n";
[download]

Thank you for your insight mr.mischief!