That's a product spec. What have you written so far, that we might help you with?

#! /usr/bin/perl -w
use strict;

open (S, "$ARGV[0]") || die "cannot open FASTA file to read: $!";

my %s;# a hash of arrays, to hold each line of sequence
my %seq; #a hash to hold the AA sequences.
my $key;

while (<S>){ #Read the FASTA file.
    chomp;

    if (/>/){
        s/>//;
        $key= $_;
    }else{
        push (@{$s{$key}}, $_);
    }

}

foreach my $a (keys %s){
    my $s= join("", @{$s{$a}});
    $seq{$a}=$s;
    #print("$a\t$s\n");
}

my @aa= qw(A R N D C Q E G H I L K M F P S T W Y V);
my $aa= join("\t", @aa);
print ("Sequence\t$aa\n");

foreach my $k (keys %seq){
    my %count; # a hash to hold the count for each amino acid in the p
+rotein.
    my @seq= split(//, $seq{$k});
    foreach my $r(@seq){
        $count{$r}++;
    }
my @row;
push(@row, $k);
    foreach my $a (@aa){
        $count{$a}||=0;
        $count{$a}= sprintf("%0.1f",($count{$a}/length($seq{$k}))*100)
+;
        push(@row,$count{$a});
    }
my $row= join("\t",@row);
print("\n$row\n");
}
[download]

this is the code but it is giving percentage output but i need in decimal

yuvraj_ghaly:

It looks like your problem is on line 42. Just stop converting the values to percentages, convert them instead to the format you want.

...roboticus

When your only tool is a hammer, all problems look like your thumb.

As the previous poster has said, you have not given us much to go on, but if you are just starting out and have nothing so far, here's a plan of attack for the problem

One way to do it is to write your own routine which would read FASTA format and then simply greps or counts the number of amino acids. This is not the recommended way however!

A better way is to look on CPAN and see if someone has done some or all of the work for you.Bio::DB:Fasta and Bio::SeqIO, FastaParse and Bio::Phylo::IO are all starting points for reading FASTA files and parsing FASTA data.

If you don't want percentages, you can just modify the last $count line:

$count{$a}= sprintf("%0.1f",($count{$a}/length($seq{$k}))*100);
[download]

$count{$a}= sprintf("%0.6f",($count{$a}/length($seq{$k})));
[download]

see the problem is I don't want any decimal. This code do division calculation between amino acid counted to overall length of sequence. I just require the amino acid counted.

Well then replace the line I mentioned above with:

 count{$a};