This may work: (UNTESTED) 

open my $out_file, '>', 'aa_report.txt' or die "Cannot open 'aa_report
+.txt' because: $!";

print 'PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename or die "Cannot open '$prot_file
+name' because: $!";

$/ = ''; # Set paragraph mode

while ( my $para = <$PROTFILE> ) {
    # Remove fasta header line
    $para =~ s/^>.*//m;
    # Remove comment line(s)
    $para =~ s/^\s*#.*//mg;

    my %prot;
    $para =~ s/([A-Z])/ ++$prot{ $1 } /eg;

    print $out_file join( ' ', map "$_=$prot{$_}", sort keys %prot ), 
+"\n";
    }

[download]

In reply to Re: how to read input from a file, one section at a time? by jwkrahn
in thread how to read input from a file, one section at a time? by davi54

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