thankz mate

modification of this code is done here but error is showing only in counting "aromatic residue"

any suggestions

#!/usr/bin/env perl

use 5.010;
use strict;
use warnings;
use autodie;

my $header = '';
my (@headers_found, %header_data);

open my $fasta_fh, '<', $ARGV[0];

while (<$fasta_fh>) {
    chomp;
    next if /^\s*($|#)/;
    
    
    if (/^>(.*)$/) {
        push @headers_found, ($header = $1);
    }
    else {
        die 'Sequence data found without a header!' unless $header; 
        
        for (split '', "\U$_") { 
           /(?<a>[BDEZ])|(?<b>[KRH])|(?<ali>[AVLI])|(?<aro>[FHYW])|(?<
+po>[DEHKNQRSTZ])|(?<nonpo>[ACFGILMPVWY])/;
           if ($_ =~ /(?<u>[XUGJOP])/){ next;}
            ++$header_data{$header}{(keys %+)[0]};
        }
              
    }
}

close $fasta_fh;

for (@headers_found) {
    say "Header: $_";
    say "\tAcidic:  $header_data{$_}{a}";
    say "\tBasic:   $header_data{$_}{b}";
    say "\tAliphatic: $header_data{$_}{ali}";
    say "\tAromatic: $header_data{$_}{aro}";
    say "\tPolar: $header_data{$_}{po}";
    say "\tNonpolar: $header_data{$_}{nonpo}";
    
#    say "\tUnknown: $header_data{$_}{u}";
    }
[download]

I haven't really done anything to it, but it works for me.

Using this fasta file:

>DROTME_HH_Q02936 
MRHIAHTQRCLSRLTSLVALLLIVLPMVFSPAHSCGPGRGLGRHRARNLY
PLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDE
>DROME_HH_Q02937 
MRHIAHTQRCLSRLTSLVALLLIVLPMVFSPAHSCGPGRGLGRHRARNLY
PLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDEE
GTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLTTTTTTESWDEDYHHGQ
YEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
ESLH
>DROME_HH_Q02938 
GTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLTTTTTTESWDEDYHHGQ
YEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSS
ESLH

And this code (essentially the same as you've posted):

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

my $header = '';
my (@headers_found, %header_data);
open my $fasta_fh, '<', $ARGV[0];
while (<$fasta_fh>) 
    {
        chomp;
        next if /^\s*($|#)/;
        
        if (/^>(.*)$/) 
            {
                push @headers_found, ($header = $1);
            }
        else 
            {
                die 'Sequence data found without a header!' unless $he
+ader; 
                for (split '', "\U$_") 
                    { 
                       /(?<a>[BDEZ])|(?<b>[KRH])|(?<ali>[AVLI])|(?<aro
+>[FHYW])|(?<po>[DEHKNQRSTZ])|(?<nonpo>[ACFGILMPVWY])/;
                       if ($_ =~ /(?<u>[XUGJOP])/){ next;}
                        ++$header_data{$header}{(keys %+)[0]};
                    }
            }
    }
close $fasta_fh;

for (@headers_found) 
    {
        print STDERR "\n\nHeader: $_";
        print STDERR "\nAcidic:  $header_data{$_}{a}";
        print STDERR "\nBasic:   $header_data{$_}{b}";
        print STDERR "\nAliphatic: $header_data{$_}{ali}";
        print STDERR "\nAromatic: $header_data{$_}{aro}";
        print STDERR "\nPolar: $header_data{$_}{po}";
        print STDERR "\nNonpolar: $header_data{$_}{nonpo}";
        print STDERR "\nUnknown: $header_data{$_}{u}" if defined $head
+er_data{$_}{u};
    }
[download]

I get this output:

Header: DROTME_HH_Q02936 
Acidic:  7
Basic:   18
Aliphatic: 31
Aromatic: 6
Polar: 19
Nonpolar: 4

Header: DROME_HH_Q02937 
Acidic:  22
Basic:   35
Aliphatic: 56
Aromatic: 16
Polar: 44
Nonpolar: 9

Header: DROME_HH_Q02938 
Acidic:  14
Basic:   17
Aliphatic: 25
Aromatic: 10
Polar: 25
Nonpolar: 5

If you're not getting that result, then post the error message that you get.

This works fine now. However it is not giving any output file as required.

 perl count_aa.pl <filename> >> <output file>

this is the command i used in console screen. If i want to get output in a file, it is not working

This is the sample fasta file for which program gives wrong calculation. I have manually counted the residues which does not correspond to program output
for Aromatic residues:
A 37
V 10
L 12
I 6
Total= 65 for polar residues:
D 12
E 7
H 2
K 12
N 3
Q 4
R 20
S 7
T 4
Z 0
Total= 71
for nonpolar residues:
A 37
C 3
F 2
G 17
I 6
L 12
M 3
P 13
V 10
W 3
Y 1
Total= 107


if you run the program using this sequence you will find the error.