Hello everyone, I have a script where I read entries from a file, one at a time. I want to count the number of alphabets in each entry, length of each entry, etc. (code attached below). My script works fine for everything else, but it does not return me the length of the entry in the '$len' variable. So, for example, if the the length if the first entry has 235 letters, I want it to return the output as "Sequence length = 235", and so on. The script runs without any error but doesn't generate an output for the length. Can anybody tell me what I'm doing wrong?

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

print 'Please enter protein sequence filename: ';
chomp( my $prot_filename = <STDIN> );

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

my $report_name = $prot_filename.'_report';
open my $out_file, '>', $report_name
     or die "Cannot open '$report_name' because: $!";

$/ = ''; # Set paragraph mode

my @count=();
my %absent=();
my $name;
my $len;

while ( my $para = <$PROTFILE> ) {
    # Remove fasta header line
    if ( $para =~ s/^>(.*)//m ){
      $name = $1;
    };
    # Remove comment line(s)
    $para =~ s/^\s*#.*//mg;

    #Remove trailing spaces between text
    #$space =~ s/\s+$//;

    my %prot;
    $para =~ s/([ACDEFGHIKLMNPQRSTVWY])/ ++$prot{ $1 } /eg;
    $len = length($para);
    
    my $num = scalar keys %prot;
    push @count,[$num,$name];
    printf "Counted %d for %s ..\n",$num,substr($name,0,50);
    
    print $out_file "$name\n";
    print $out_file join( ' ', map "$_=$prot{$_}", sort keys %prot ), 
+"\n";
    printf $out_file "Amino acid alphabet = %d\n\n",$num ;
    print $out_file "Sequence length = ", $len;
    
    # count absent
    for ('A'..'Z'){
      ++$absent{$_} unless exists $prot{$_};
    };
     
};

# sort names by count in ascending order to get lowest
my @sorted = sort { $a->[0] <=> $b->[0] } @count;
my $lowest = $sorted[0]->[0];

# maybe more than 1 lowest
printf $out_file "Least number of amino acids is %d in these entries\n
+",$lowest;
my @lowest = grep { $_->[0] == $lowest } @sorted;
print $out_file "$_->[1]\n" for @lowest;

# show all results
print $out_file "\nAll results in ascending count\n";
for (@sorted){
  printf $out_file "%d  %s\n",@$_;
};
close $out_file;
print "Results are printed in $report_name\n";

# print absent counts
print "\nExclusion of various amino acids in $prot_filename is as foll
+ows\n";
for (sort keys %absent){
  printf "%s=%d\n",$_,$absent{$_};
};
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