#! /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

In reply to Re^2: Counting amino acids by yuvraj_ghaly
in thread Counting amino acids by yuvraj_ghaly

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