Hi, here is one solution. I'm using Path::Tiny for file handling. Also localizing the special variable $/ (the input record separator), as you hinted at.

use strict; use warnings; use feature 'say';
use Path::Tiny;

local $/ = '>';

my $fh = path('./foo.fasta')->openr;

while ( my $paragraph = <$fh> ) {
    chomp $paragraph;
    my @lines = split /\n/, $paragraph or next;
    my ( $identifier, $string );
    for my $line ( @lines ) {
        if ( $line =~ /(sequence\d+)/ ) {
            $identifier = $1;
        } else {
            $string .= $line;
        }
    }
    say "$identifier\t$string";
}

__END__
[download]

>sequence1
ACTCCCCGTGCGCGCCCGGCCCGTAGCGTCCTCGTCGCCGCCCCTCGTCTCGCAGCCGCAGCCCGCGTGG
ACGCTCTCGCCTGAGCGCCGCGGACTAGCCCGGGTGGCC

> sequence2
CAGTCCGGCAGCGCCGGGGTTAAGCGGCCCAAGTAAACGTAGCGCAGCGATCGGCGCCGGAGATTCGCGA
ACCCGACACTCCGCGCCGCCCGCCGGCCAGGACCCGCGGCGCGATCGCGGCGCCGCGCTACAGCCAGCCT
CACTGGCGCGCGGGCGAGCGCACGGGCGCTC

>randomstuff sequence3
CACGACAGGCCCGCTGAGGCTTGTGCCAGACCTTGGAAACCTCAGGTATATACCTTTCCAGACGCGGGAT
CTCCCCTCCCC

> sequence4 blahblah
CAGCAGACATCTGAATGAAGAAGAGGGTGCCAGCGGGTATGAGGAGTGCATTATCGTTAATGGGAACTTC
AGTGACCAGTCCTCAGACACGAAGGATGCTCCCTCACCCCCAGTCTTGGAGGCAATCTGCACAGAGCCAG
TCTGCACACC
[download]

$ perl foo.pl
sequence1    ACTCCCCGTGCGCGCCCGGCCCGTAGCGTCCTCGTCGCCGCCCCTCGTCTCGCAGCC
+GCAGCCCGCGTGGACGCTCTCGCCTGAGCGCCGCGGACTAGCCCGGGTGGCC
sequence2    CAGTCCGGCAGCGCCGGGGTTAAGCGGCCCAAGTAAACGTAGCGCAGCGATCGGCGC
+CGGAGATTCGCGAACCCGACACTCCGCGCCGCCCGCCGGCCAGGACCCGCGGCGCGATCGCGGCGCCGC
+GCTACAGCCAGCCTCACTGGCGCGCGGGCGAGCGCACGGGCGCTC
sequence3    CACGACAGGCCCGCTGAGGCTTGTGCCAGACCTTGGAAACCTCAGGTATATACCTTT
+CCAGACGCGGGATCTCCCCTCCCC
sequence4    CAGCAGACATCTGAATGAAGAAGAGGGTGCCAGCGGGTATGAGGAGTGCATTATCGT
+TAATGGGAACTTCAGTGACCAGTCCTCAGACACGAAGGATGCTCCCTCACCCCCAGTCTTGGAGGCAAT
+CTGCACAGAGCCAGTCTGCACACC
[download]

Hope this helps!

Thank you! This was indeed helpful. :)

This appears to do what you require:

#!/usr/bin/perl
# fasta_to_tbl.pl
use strict;
use warnings;

die "Please specify suitable file\n" if @ARGV != 1;
my ( $fasta ) = @ARGV;

my $outfile = "$fasta.tbl";

open my $in,  '<', $fasta   or die "error reading $fasta. $!";
open my $out, '>', $outfile or die "error creating $outfile. $!";


while ( <$in> ) {
    if ( /^>/ ) {
        # Identifier!
        # "\t" TAB character for "tabular format"
        s/[:\s|,;].*/\t/s;
        print $out $_;
        next;
        }
    s/\s//g;
    if ( !/\w/ || eof $in ) {
        # empty line or end of file
        print $out "$_\n\n";
        }
    else {
        # Data
        print $out $_;
        }
    }
[download]

Thank you! This is helpful!

G'day rarenas,

Welcome to the Monastery.

I'd probably use a technique more along these lines:

#!/usr/bin/env perl

use 5.014;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        substr $_, 0, 1, '' if $. == 1;
        my ($head, $seq) = split /\n/, $_, 2;
        printf "%-15s %s\n", $head, $seq =~ y/\n//dr;
    }
}

__DATA__
>SEQ1
AAA
>SEQ2
AAA
CCC

>SEQ3

AAA
CCC
GGG

>SEQ4 plus ...
AAA
CCC
GGG
TTT
[download]

Output:

SEQ1            AAA
SEQ2            AAACCC
SEQ3            AAACCCGGG
SEQ4 plus ...   AAACCCGGGTTT
[download]

Notes:

• If you are the Anonymous Monk to whom I responded with "Re: unique sequences" (a couple of days ago), some of that code should look familiar. If you're not that person, or just need a revision, see that post for actual I/O and links to documentation for various elements used in this post.
• See "perl5140delta: Non-destructive substitution" for the 'r' modifier I've used with y///. If you're using a Perl version earlier than 5.14, you'll need to do the transliteration (or transobliteration as it's been called when the 'd' modifier is used) as a separate step prior to printf.

Thank you Ken!

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


while (my $line = <DATA>)
{
    process_record($line) if $line=~ /^>/;
}

sub process_record
{
    my $line = shift;
    $line =~ s/\s*$//;  #or chomp $line
    print "$line\t";
    
    while (defined ($line=<DATA>) and $line !~ /^\s*$/)
    {
        $line =~ s/\s*$//;  #or chomp $line
        print $line;
    }
    print "\n";
}

=Prints:
>sequence1    ACTCCCCGTGCGCGCCCGGCCCGTAGCGTCCTCGTCGCCGCCCCTCGTCTCGCAGC
+CGCAGCCCGCGTGGACGCTCTCGCCTGAGCGCCGCGGACTAGCCCGGGTGGCC
>sequence2    CAGTCCGGCAGCGCCGGGGTTAAGCGGCCCAAGTAAACGTAGCGCAGCGATCGGCG
+CCGGAGATTCGCGAACCCGACACTCCGCGCCGCCCGCCGGCCAGGACCCGCGGCGCGATCGCGGCGCCG
+CGCTACAGCCAGCCTCACTGGCGCGCGGGCGAGCGCACGGGCGCTC
>sequence3    CACGACAGGCCCGCTGAGGCTTGTGCCAGACCTTGGAAACCTCAGGTATATACCTT
+TCCAGACGCGGGATCTCCCCTCCCC
>sequence4    CAGCAGACATCTGAATGAAGAAGAGGGTGCCAGCGGGTATGAGGAGTGCATTATCG
+TTAATGGGAACTTCAGTGACCAGTCCTCAGACACGAAGGATGCTCCCTCACCCCCAGTCTTGGAGGCAA
+TCTGCACAGAGCCAGTCTGCACACC
=cut



__DATA__
>sequence1
ACTCCCCGTGCGCGCCCGGCCCGTAGCGTCCTCGTCGCCGCCCCTCGTCTCGCAGCCGCAGCCCGCGTGG
ACGCTCTCGCCTGAGCGCCGCGGACTAGCCCGGGTGGCC

>sequence2
CAGTCCGGCAGCGCCGGGGTTAAGCGGCCCAAGTAAACGTAGCGCAGCGATCGGCGCCGGAGATTCGCGA
ACCCGACACTCCGCGCCGCCCGCCGGCCAGGACCCGCGGCGCGATCGCGGCGCCGCGCTACAGCCAGCCT
CACTGGCGCGCGGGCGAGCGCACGGGCGCTC

>sequence3
CACGACAGGCCCGCTGAGGCTTGTGCCAGACCTTGGAAACCTCAGGTATATACCTTTCCAGACGCGGGAT
CTCCCCTCCCC

>sequence4
CAGCAGACATCTGAATGAAGAAGAGGGTGCCAGCGGGTATGAGGAGTGCATTATCGTTAATGGGAACTTC
AGTGACCAGTCCTCAGACACGAAGGATGCTCCCTCACCCCCAGTCTTGGAGGCAATCTGCACAGAGCCAG
TCTGCACACC
[download]

    (my $id) = $line =~ /^(>\w+)/;  #allow for kruft after id
    print "$id\t";
[download]

Thanks for the response! The multi fasta file I put up is a very simple file but I know, from working with fasta files, that sometimes the titles can be complex and may be divided in strange ways. Sometimes there isn't a space between the name and the rest of the information but instead other symbols that can be used as separators. That's the reason why I had all those non-word symbols. But, as you say, it is not necessary if I know what I want to throw away. This really helps! Thanks again!

Thank you all for responding. All your responses were helpful. I find it funny that what I needed was so short and simple in code. Have a lot to learn. Thanks again! :)

If you are working in this field you may be interested in bioperl.