Using Bio::SeqIO, you can do something like this: 
#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file   => "fasta_junk.txt" ,
                           -format => 'fasta');
my $out = Bio::SeqIO->new( -file   => '>o33.txt',#note the leading '>'
                           -format => 'fasta');

my $i;

while ( my $seq = $in->next_seq() ) {
    $seq->display_id(++$i); # set 'id' equal to 1, 2, ...
    $out->write_seq($seq);
}

__END__
*** fasta_junk.txt
>GJKKTUG01DYDGC
GGGTATTCCTTCTCCACCTTGCAGCTAACATCAGTGTTTCGTCTACTCAAGCACGCCAAC
ACGCCCTAGAGCGCCCTGTCCAGGGGATGGCAACCAACTCTGACCCTGCAAGTGCAGCAG
ACATGAGGAATACAAACTACAATCTTTTACTTGATGATGCAATGCCGGACAAACTCTAGA
>F0Z7V0F01EDB3V
AAGGCGAGNGGTATCACGCAGTAAGTTACGGTTTTCGGGTAACGCGTCNGNGGNACTAAC
CCACGGNGGGTAACCCGTCNCTACCGGTATAGGACTAAGGTTACCGGAACGTCGTGGGGT
ACCCCCCGGACGGGGACCGTCCCCTCATANAGTCAACNGTNTGAGATGGACTAACTCAAA
CCTAGTTTCAAGTACTATTTAACTTACTTACGTTACCCGTAATTTCGGCGTTTAGAGGCG

*** o33.txt
>1
GGGTATTCCTTCTCCACCTTGCAGCTAACATCAGTGTTTCGTCTACTCAAGCACGCCAAC
ACGCCCTAGAGCGCCCTGTCCAGGGGATGGCAACCAACTCTGACCCTGCAAGTGCAGCAG
ACATGAGGAATACAAACTACAATCTTTTACTTGATGATGCAATGCCGGACAAACTCTAGA
>2
AAGGCGAGNGGTATCACGCAGTAAGTTACGGTTTTCGGGTAACGCGTCNGNGGNACTAAC
CCACGGNGGGTAACCCGTCNCTACCGGTATAGGACTAAGGTTACCGGAACGTCGTGGGGT
ACCCCCCGGACGGGGACCGTCCCCTCATANAGTCAACNGTNTGAGATGGACTAACTCAAA
CCTAGTTTCAAGTACTATTTAACTTACTTACGTTACCCGTAATTTCGGCGTTTAGAGGCG

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In reply to Re: rename FASTA by Cristoforo
in thread rename FASTA by naka

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